@atoms-tech/atoms-mcp 0.23.0 → 0.25.2

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Files changed (6) hide show
  1. package/dist/apps/src/apps/browse/browse-app.html +1 -1
  2. package/dist/apps/src/apps/editor/editor-app.html +6 -6
  3. package/dist/apps/src/apps/trace/trace-app.html +1 -1
  4. package/dist/index.cjs +1 -1
  5. package/dist/index.js +1 -1
  6. package/package.json +4 -2
package/dist/index.cjs CHANGED
@@ -1,2 +1,2 @@
1
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  #!/usr/bin/env node
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- "use strict";var e=require("fs/promises"),t=require("os"),r=require("path"),i=require("@supabase/supabase-js"),n=require("http"),a=require("crypto"),s=require("url"),o=require("zod"),d=require("@modelcontextprotocol/ext-apps/server"),c=require("@modelcontextprotocol/sdk/server/mcp.js"),l=require("module"),m=require("@modelcontextprotocol/sdk/server/stdio.js"),p="undefined"!=typeof document?document.currentScript:null;function u(e){return e&&e.__esModule?e:{default:e}}var _,f,h,g,y,w,b,v=u(e),j=u(r),S=u(a),x=Object.defineProperty,k=Object.getOwnPropertyNames,E=(e,t,r)=>function(){if(r)throw r[0];try{return e&&(t=(0,e[k(e)[0]])(e=0)),t}catch(e){throw r=[e],e}},I=(e,t)=>{for(var r in t)x(e,r,{get:t[r],enumerable:!0})};function A(e){return b.get(e)}var R=E({"src/core/tool-catalog.ts"(){_=new Set(["atoms_status","atoms_list_projects"]),f=new Set(["atoms_create_item","atoms_update_item","atoms_delete_item","atoms_restore_item","atoms_link_items","atoms_bulk_import","atoms_record_test_result","atoms_record_test_results","atoms_create_variable","atoms_update_variable","atoms_delete_variable","atoms_create_domain","atoms_update_domain","atoms_delete_domain","atoms_create_level","atoms_create_field","atoms_delete_field","atoms_reorder_fields","atoms_create_baseline","atoms_lock_baseline","atoms_restore_baseline","atoms_create_analysis","atoms_fill_row","atoms_link_mitigation"]),h=new Set(["atoms_delete_item","atoms_delete_variable","atoms_delete_domain","atoms_delete_field","atoms_restore_baseline"]),g=new Set(["atoms_bulk_import"]),y={items:["atoms_list_items","atoms_get_item","atoms_search","atoms_semantic_search","atoms_browse","atoms_get_history","atoms_create_item","atoms_update_item","atoms_delete_item","atoms_restore_item","atoms_bulk_import"],traceability:["atoms_trace","atoms_link_items","atoms_export_mermaid","atoms_impact_analysis"],coverage:["atoms_get_coverage","atoms_verification_status","atoms_record_test_result","atoms_record_test_results","atoms_project_summary","atoms_list_assets"],variables:["atoms_list_variables","atoms_get_variable","atoms_create_variable","atoms_update_variable","atoms_delete_variable"],domains:["atoms_list_domains","atoms_create_domain","atoms_update_domain","atoms_delete_domain","atoms_list_levels","atoms_create_level","atoms_list_fields","atoms_create_field","atoms_delete_field","atoms_reorder_fields"],baselines:["atoms_list_baselines","atoms_create_baseline","atoms_lock_baseline","atoms_diff_baselines","atoms_restore_baseline"],analysis:["atoms_create_analysis","atoms_fill_row","atoms_get_analysis","atoms_link_mitigation","atoms_get_gaps"]},w=Object.keys(y),b=new Map;for(const[e,t]of Object.entries(y))for(const r of t)b.set(r,e)}});function O(e,t){if(_.has(t))return{allowed:!0};if(e.lockdown&&!new Set(["atoms_list_items","atoms_get_item","atoms_search","atoms_browse"]).has(t))return{allowed:!1,reason:"lockdown"};if(e.forbidden_tools.includes(t))return{allowed:!1,reason:"forbidden_tool"};if(e.read_only&&f.has(t))return{allowed:!1,reason:"read_only"};if(e.block_destructive&&h.has(t))return{allowed:!1,reason:"block_destructive"};if(e.block_bulk_import&&g.has(t))return{allowed:!1,reason:"block_bulk_import"};const r=A(t);return void 0===r||e.allowed_toolsets.includes(r)?{allowed:!0}:{allowed:!1,reason:"toolset_disabled"}}function D(e,t){return O(e,t).allowed}function z(e){switch(e){case"lockdown":return"MCP is in lockdown mode for your role — only read-only browse is available.";case"read_only":return"Your org policy puts MCP in read-only mode. Mutating tools are not exposed.";case"block_destructive":return"Your org policy blocks destructive operations (delete tools).";case"block_bulk_import":return"Your org policy blocks bulk import.";case"forbidden_tool":return"This tool is on your org's forbidden list.";case"toolset_disabled":return"This tool's toolset is not enabled in your org policy."}}var H,U,C,q,T=E({"src/core/policy.ts"(){R()}}),M=E({"src/core/types.ts"(){H={read_only:!1,lockdown:!1,block_destructive:!1,block_bulk_import:!1,cross_project_browse:!0,allowed_toolsets:["items","traceability","coverage","variables","domains","baselines"],forbidden_tools:[],project_scope:null,require_confirmation_for:[]},U={read_only:!0,lockdown:!0,block_destructive:!0,block_bulk_import:!0,cross_project_browse:!1,allowed_toolsets:[],forbidden_tools:[],project_scope:[],require_confirmation_for:[]}}});function P(){return C}var $=E({"src/middleware/session-policy.ts"(){M(),C=H,q=null}});function N(){const e=process.env.ATOMS_MCP_TOOLSETS?.trim();if(!e)return null;const t=e.split(",").map(e=>e.trim()).filter(Boolean);if(0===t.length)return null;const r=new Set,i=[];for(const e of t)w.includes(e)?r.add(e):i.push(e);return{allowed:r,unknown:i}}function L(){const e=process.env.ATOMS_MCP_READ_ONLY;return"1"===e||"true"===e?.toLowerCase()}function F(e){if(L()&&f.has(e))return!1;if(_.has(e))return!0;const t=N();if(null===t)return D(P(),e);const r=A(e);return!!r&&!!t.allowed.has(r)&&D(P(),e)}var W,V,B=E({"src/middleware/tool-registry.ts"(){R(),T(),$()}}),J={};async function Q(){try{const t=await e.readFile(V,"utf-8"),r=JSON.parse(t);return r.access_token&&r.refresh_token?r:null}catch{return null}}async function G(t){await e.mkdir(W,{recursive:!0,mode:448}),await e.writeFile(V,JSON.stringify(t,null,2),{mode:384})}async function Y(){const e=await Q();return!!e&&e.expires_at>Date.now()+6e4}function K(e){return e.expires_at>Date.now()+6e4}async function Z(){try{await e.unlink(V)}catch{}}function X(){return V}I(J,{clearCredentials:()=>Z,getCredentialsPath:()=>X,hasValidCredentials:()=>Y,isTokenValid:()=>K,readCredentials:()=>Q,writeCredentials:()=>G});var ee,te,re,ie,ne,ae,se,oe=E({"src/auth/token-store.ts"(){W=r.join(t.homedir(),".atoms"),V=r.join(W,"credentials.json")}}),de={};async function ce(){try{await e.mkdir(ee,{recursive:!0,mode:448});const t=await e.open(te,"wx");try{await t.writeFile(`${process.pid} ${Date.now()}`)}finally{await t.close()}return!0}catch(e){if("EEXIST"===e.code)return!1;throw e}}async function le(){try{await e.unlink(te)}catch{}}async function me(){try{const t=await e.stat(te);return Date.now()-t.mtimeMs>re}catch{return!1}}async function pe(e,t,r=se){const i=r.now()+ie;for(;;){if(await r.tryAcquire())try{try{return await e()}catch{}return await t()}finally{await r.release()}try{return await e()}catch{}if(await r.isStale())await r.release();else{if(r.now()>i)return await t();await r.wait(ne)}}}I(de,{runExclusiveAuth:()=>pe});var ue,_e,fe,he=E({"src/auth/lock.ts"(){ee=r.join(t.homedir(),".atoms"),te=r.join(ee,".auth.lock"),re=7e4,ie=12e4,ne=300,ae=e=>new Promise(t=>setTimeout(t,e)),se={now:Date.now,wait:ae,tryAcquire:ce,release:le,isStale:me}}}),ge={};function ye(e){return e.trim().replace(/\/+$/,"")}I(ge,{ATOMS_APP_URL:()=>fe,ATOMS_SUPABASE_ANON_KEY:()=>_e,ATOMS_SUPABASE_URL:()=>ue,resolveUrl:()=>ye});var we=E({"src/config.ts"(){ue=ye(process.env.ATOMS_SUPABASE_URL??"https://gmebjyhomsbvhrxffzre.supabase.co"),_e=process.env.ATOMS_SUPABASE_ANON_KEY??"sb_publishable_b49MUAB8XCrQiF7x5b9lUA_w1aplSBH",fe=process.env.ATOMS_APP_URL??"https://atoms.tech"}}),be={};async function ve(){const e=process.env.ATOMS_ACCESS_TOKEN;if(e){const t=Se(e);return{access_token:e,refresh_token:"",user_id:t.sub,email:t.email??""}}const t=await Q();if(t&&t.expires_at>Date.now()+6e4){const e=Se(t.access_token);return{access_token:t.access_token,refresh_token:t.refresh_token,user_id:e.sub,email:e.email??t.user_email??""}}return null}async function je(){const e=await ve();if(e)return e;const t=await Q();if(!t)throw new Error("Not authenticated. Run 'npx @atoms-tech/atoms-mcp login' to connect your ATOMS account.");return pe(async()=>{const e=await ve();if(e)return e;throw new Error("no fresh token yet")},()=>async function(e){process.stderr.write("[atoms-mcp] Refreshing access token...\n");const t=i.createClient(ue,_e);let r=await t.auth.refreshSession({refresh_token:e.refresh_token});if(r.error||!r.data.session){const i=await Q();if(i&&i.expires_at>Date.now()+6e4){const e=Se(i.access_token);return{access_token:i.access_token,refresh_token:i.refresh_token,user_id:e.sub,email:e.email??i.user_email??""}}i&&i.refresh_token&&i.refresh_token!==e.refresh_token&&(process.stderr.write("[atoms-mcp] Refresh token was rotated by another session; retrying with the latest...\n"),r=await t.auth.refreshSession({refresh_token:i.refresh_token}))}if(r.error||!r.data.session){const e=r.error?[r.error.status,r.error.message].filter(Boolean).join(" ").trim():"no session returned";throw new Error(`Token refresh failed (${e}). Your saved ATOMS session is no longer valid — re-run 'npx @atoms-tech/atoms-mcp login'.`)}const n=r.data.session;return await G({access_token:n.access_token,refresh_token:n.refresh_token,expires_at:Date.now()+1e3*(n.expires_in??3600),user_email:n.user?.email}),{access_token:n.access_token,refresh_token:n.refresh_token,user_id:n.user?.id??"",email:n.user?.email??""}}(t))}function Se(e){const t=e.split(".");if(3!==t.length)throw new Error("Invalid JWT format");const r=t[1].replace(/-/g,"+").replace(/_/g,"/").padEnd(t[1].length+(4-t[1].length%4)%4,"="),i=JSON.parse(Buffer.from(r,"base64").toString("utf-8"));if(!i.sub)throw new Error("JWT missing 'sub' claim");return i}I(be,{getValidToken:()=>je,readValidToken:()=>ve});var xe,ke,Ee,Ie,Ae,Re=E({"src/auth/refresh.ts"(){oe(),he(),we()}}),Oe={};async function De(){if(xe)try{const e=await Q();e&&e.expires_at>Ae&&(process.stderr.write("[atoms-mcp] Credentials file refreshed elsewhere — rebuilding client.\n"),ze())}catch{}if(xe&&Ie>Date.now()+6e4)return xe;xe&&process.stderr.write("[atoms-mcp] Token expiring, refreshing client...\n");const{access_token:e,user_id:t,email:r}=await je(),n=e.split(".");if(3===n.length)try{const e=JSON.parse(Buffer.from(n[1].replace(/-/g,"+").replace(/_/g,"/"),"base64").toString());Ie=1e3*(e.exp??0)}catch{Ie=Date.now()+36e5}try{const e=await Q();Ae=e?.expires_at??0}catch{Ae=0}const a=i.createClient(ue,_e,{global:{headers:{Authorization:`Bearer ${e}`}}});return ke=t,Ee=r,xe=a}function ze(){xe=null,ke=null,Ee=null,Ie=0,Ae=0}function He(e){let t="";if(e instanceof Error)t=e.message;else if(e&&"object"==typeof e){const r=e;t="string"==typeof r.message?r.message:"string"==typeof r.code?r.code:String(e)}else null!=e&&(t=String(e));return/jwt\s*expired|invalid.?jwt|token.*(?:has\s+)?expired|jwt.*invalid|pgrst301/i.test(t)}async function Ue(e){try{return await e()}catch(t){if(!He(t))throw t;return process.stderr.write("[atoms-mcp] Data tier rejected JWT — invalidating client and retrying once.\n"),ze(),await e()}}function Ce(){if(!ke)throw new Error("Not authenticated. Call getClient() first.");return ke}function qe(){return Ee??""}async function Te(e,t){const r=Ce(),{data:i,error:n}=await e.from("projects").select("org_id").eq("id",t).maybeSingle();if(n||!i)throw new Error(`Project '${t}' not found`);const{data:a,error:s}=await e.from("org_members").select("role").eq("user_id",r).eq("org_id",i.org_id).maybeSingle();if(s||!a){const{data:t}=await e.rpc("is_platform_admin");if(!0===t)return"admin";throw new Error("Not a member of this project's organization")}if("viewer"===a.role)throw new Error("VIEWER_ROLE");return a.role}async function Me(e,t){const r=Ce(),{data:i,error:n}=await e.from("projects").select("org_id, created_by").eq("id",t).maybeSingle();if(n||!i)throw new Error(`Project '${t}' not found`);const{data:a,error:s}=await e.from("org_members").select("role").eq("user_id",r).eq("org_id",i.org_id).maybeSingle();if(s||!a)throw new Error("Not a member of this project's organization");if("admin"===a.role)return"admin";if(i.created_by===r)return"owner";throw new Error("PROJECT_FIELD_ADMIN_OR_OWNER_REQUIRED")}I(Oe,{getClient:()=>De,getUserEmail:()=>qe,getUserId:()=>Ce,invalidateClient:()=>ze,isJwtExpiredError:()=>He,requireProjectFieldDefinitionAccess:()=>Me,requireWriteAccess:()=>Te,withJwtRetry:()=>Ue});var Pe,$e,Ne=E({"src/db/client.ts"(){Re(),oe(),we(),xe=null,ke=null,Ee=null,Ie=0,Ae=0}}),Le={};async function Fe(){const e=a.randomBytes(32).toString("base64url"),t=a.createHash("sha256").update(e).digest("base64url"),r=`http://localhost:${Pe}${$e}`,i=new s.URL(`${fe}/auth/mcp-consent`);return i.searchParams.set("redirect_uri",r),i.searchParams.set("code_challenge",t),i.searchParams.set("code_challenge_method","S256"),new Promise((t,r)=>{let a;function o(){clearTimeout(a)}const d=n.createServer(async(i,n)=>{const a=new s.URL(i.url??"/",`http://localhost:${Pe}`);if(a.pathname!==$e)return n.writeHead(404),void n.end("Not found");try{if("access_denied"===a.searchParams.get("error"))return n.writeHead(200,{"Content-Type":"text/html"}),n.end(Ve("Authorization was cancelled.")),o(),d.close(),void r(new Error("Authorization cancelled by user."));const i=a.searchParams.get("code");if(i){const a=await fetch(`${ue}/auth/v1/token?grant_type=pkce`,{method:"POST",headers:{"Content-Type":"application/json",apikey:_e},body:JSON.stringify({auth_code:i,code_verifier:e})}),s=await a.json();if(!a.ok||!s.access_token){const e=s.error_description??s.msg??"Unknown error";return n.writeHead(200,{"Content-Type":"text/html"}),n.end(Ve(`Code exchange failed: ${e}`)),o(),d.close(),void r(new Error(`Code exchange failed: ${e}`))}let c="authenticated";try{c=JSON.parse(Buffer.from(s.access_token.split(".")[1],"base64").toString()).email??c}catch{}const{createClient:l}=await import("@supabase/supabase-js"),m=l(ue,_e,{global:{headers:{Authorization:`Bearer ${s.access_token}`}}}),{data:p,error:u}=await m.from("org_members").select("org_id").limit(1);return u||!p||0===p.length?(n.writeHead(200,{"Content-Type":"text/html"}),n.end(Ve('No ATOMS account found for this Google account.<br><br>Please sign up at <a href="https://atoms.tech">atoms.tech</a> first, then run this login command again.')),o(),d.close(),void r(new Error("No ATOMS account found. Sign up at atoms.tech first."))):s.refresh_token?(await G({access_token:s.access_token,refresh_token:s.refresh_token,expires_at:Date.now()+1e3*(s.expires_in??3600),user_email:c}),n.writeHead(200,{"Content-Type":"text/html"}),n.end(We(c)),o(),d.close(),void t({email:c})):(n.writeHead(200,{"Content-Type":"text/html"}),n.end(Ve("Sign-in succeeded but no refresh token was issued, so the session would expire within the hour. This usually points to a Supabase Auth setting (refresh-token rotation or session policy). Please contact ATOMS support.")),o(),d.close(),void r(new Error("No refresh token issued by Supabase — cannot persist a durable session.")))}const s=a.searchParams.get("access_token"),c=a.searchParams.get("refresh_token"),l=parseInt(a.searchParams.get("expires_in")??"3600",10);s&&c?(await G({access_token:s,refresh_token:c,expires_at:Date.now()+1e3*l}),n.writeHead(200,{"Content-Type":"text/html"}),n.end(We("authenticated")),o(),d.close(),t({email:"authenticated"})):(n.writeHead(200,{"Content-Type":"text/html"}),n.end("<!DOCTYPE html>\n<html>\n<head><title>ATOMS MCP Login</title></head>\n<body>\n <h1>Completing login...</h1>\n <script>\n const hash = window.location.hash.substring(1);\n const params = new URLSearchParams(hash);\n const data = {\n access_token: params.get('access_token'),\n refresh_token: params.get('refresh_token'),\n expires_in: params.get('expires_in'),\n user_email: ''\n };\n if (data.access_token) {\n // Decode JWT to get email\n try {\n const payload = JSON.parse(atob(data.access_token.split('.')[1]));\n data.user_email = payload.email || '';\n } catch(e) {}\n fetch('/token', {\n method: 'POST',\n headers: { 'Content-Type': 'application/json' },\n body: JSON.stringify(data)\n }).then(() => {\n document.body.innerHTML = '<h1>Login successful! You can close this tab.</h1>';\n }).catch(() => {\n document.body.innerHTML = '<h1>Login failed. Please try again.</h1>';\n });\n } else {\n document.body.innerHTML = '<h1>Login failed — no tokens received.</h1>';\n }\n <\/script>\n</body>\n</html>"))}catch(e){n.writeHead(500),n.end("Authentication failed"),o(),d.close(),r(e)}});d.on("request",async(e,i)=>{if("POST"===e.method&&"/token"===e.url){let n="";e.on("data",e=>{n+=e.toString()}),e.on("end",async()=>{try{const e=JSON.parse(n);await G({access_token:e.access_token,refresh_token:e.refresh_token,expires_at:Date.now()+1e3*(e.expires_in??3600),user_email:e.user_email}),i.writeHead(200,{"Content-Type":"application/json"}),i.end(JSON.stringify({ok:!0})),o(),d.close(),t({email:e.user_email??"authenticated"})}catch(e){i.writeHead(500),i.end("Failed to store credentials"),o(),d.close(),r(e)}})}}),d.listen(Pe,"127.0.0.1",async()=>{process.stderr.write("\nOpening browser for ATOMS login...\n"),process.stderr.write(`If the browser doesn't open, visit:\n${i.toString()}\n\n`);try{const{default:e}=await import("open");await e(i.toString())}catch{process.stderr.write("Could not open browser automatically. Please open the URL above.\n")}}),a=setTimeout(()=>{d.close(),r(new Error("Login timed out after 60 seconds. Run 'npx @atoms-tech/atoms-mcp login' to try again."))},6e4)})}function We(e){return`<!DOCTYPE html>\n<html>\n<head>\n <title>ATOMS MCP — Authorized</title>\n <style>\n * { margin: 0; padding: 0; box-sizing: border-box; }\n body {\n font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', system-ui, sans-serif;\n background: #0a0a0a;\n color: #fafafa;\n display: flex;\n align-items: center;\n justify-content: center;\n min-height: 100vh;\n }\n .card {\n background: #171717;\n border: 1px solid #262626;\n border-radius: 16px;\n padding: 48px;\n max-width: 480px;\n width: 100%;\n text-align: center;\n }\n .icon {\n width: 56px;\n height: 56px;\n background: #052e16;\n border-radius: 50%;\n display: flex;\n align-items: center;\n justify-content: center;\n margin: 0 auto 24px;\n }\n .icon svg { width: 28px; height: 28px; }\n h1 {\n font-size: 22px;\n font-weight: 600;\n margin-bottom: 8px;\n color: #22c55e;\n }\n .email {\n font-size: 14px;\n color: #a3a3a3;\n margin-bottom: 32px;\n }\n .permissions {\n text-align: left;\n background: #0a0a0a;\n border: 1px solid #262626;\n border-radius: 12px;\n padding: 20px;\n margin-bottom: 24px;\n }\n .permissions h3 {\n font-size: 12px;\n font-weight: 600;\n color: #737373;\n text-transform: uppercase;\n letter-spacing: 0.05em;\n margin-bottom: 12px;\n }\n .perm-item {\n display: flex;\n align-items: center;\n gap: 10px;\n padding: 6px 0;\n font-size: 14px;\n color: #d4d4d4;\n }\n .perm-item .dot {\n width: 6px;\n height: 6px;\n background: #22c55e;\n border-radius: 50%;\n flex-shrink: 0;\n }\n .closing {\n font-size: 13px;\n color: #525252;\n }\n .closing span { color: #a3a3a3; font-variant-numeric: tabular-nums; }\n </style>\n</head>\n<body>\n <div class="card">\n <div class="icon">\n <svg fill="none" viewBox="0 0 24 24" stroke="#22c55e" stroke-width="2.5">\n <path stroke-linecap="round" stroke-linejoin="round" d="M5 13l4 4L19 7"/>\n </svg>\n </div>\n <h1>Authorization Granted</h1>\n <p class="email">${e}</p>\n\n <div class="permissions">\n <h3>ATOMS MCP can now</h3>\n <div class="perm-item"><span class="dot"></span> Read your projects and requirements</div>\n <div class="perm-item"><span class="dot"></span> Create and edit requirements and test cases</div>\n <div class="perm-item"><span class="dot"></span> Record test results (pass/fail)</div>\n <div class="perm-item"><span class="dot"></span> Manage traceability relationships</div>\n <div class="perm-item"><span class="dot"></span> Export coverage reports and diagrams</div>\n </div>\n\n <p class="closing">This tab will close in <span id="countdown">5</span>s</p>\n </div>\n\n <script>\n let seconds = 5;\n const el = document.getElementById('countdown');\n const timer = setInterval(() => {\n seconds--;\n el.textContent = seconds;\n if (seconds <= 0) {\n clearInterval(timer);\n window.close();\n // If window.close() is blocked (not opened by script), update message\n setTimeout(() => {\n document.querySelector('.closing').textContent = 'You can close this tab now.';\n }, 500);\n }\n }, 1000);\n <\/script>\n</body>\n</html>`}function Ve(e){return`<!DOCTYPE html>\n<html>\n<head>\n <title>ATOMS MCP — Failed</title>\n <style>\n * { margin: 0; padding: 0; box-sizing: border-box; }\n body {\n font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', system-ui, sans-serif;\n background: #0a0a0a;\n color: #fafafa;\n display: flex;\n align-items: center;\n justify-content: center;\n min-height: 100vh;\n }\n .card {\n background: #171717;\n border: 1px solid #262626;\n border-radius: 16px;\n padding: 48px;\n max-width: 480px;\n width: 100%;\n text-align: center;\n }\n .icon {\n width: 56px;\n height: 56px;\n background: #450a0a;\n border-radius: 50%;\n display: flex;\n align-items: center;\n justify-content: center;\n margin: 0 auto 24px;\n }\n .icon svg { width: 28px; height: 28px; }\n h1 { font-size: 22px; font-weight: 600; margin-bottom: 16px; color: #ef4444; }\n .reason { font-size: 14px; color: #a3a3a3; line-height: 1.6; }\n .reason a { color: #7c3aed; text-decoration: underline; }\n </style>\n</head>\n<body>\n <div class="card">\n <div class="icon">\n <svg fill="none" viewBox="0 0 24 24" stroke="#ef4444" stroke-width="2.5">\n <path stroke-linecap="round" stroke-linejoin="round" d="M6 18L18 6M6 6l12 12"/>\n </svg>\n </div>\n <h1>Authorization Failed</h1>\n <p class="reason">${e}</p>\n </div>\n</body>\n</html>`}I(Le,{login:()=>Fe});var Be,Je,Qe,Ge,Ye=E({"src/auth/login.ts"(){oe(),we(),Pe=19275,$e="/callback"}});function Ke(e,t=0){if(t>5)return"[depth-limit]";if("string"==typeof e){for(const t of Qe)if(t.test(e.trim()))return"[redacted]";return e.length>Ge?e.slice(0,Ge)+"…":e}if(Array.isArray(e))return e.slice(0,20).map(e=>Ke(e,t+1));if(null!==e&&"object"==typeof e){const r={};for(const[i,n]of Object.entries(e)){const e=i.toLowerCase();Be.has(e)?r[i]="[redacted]":Je.has(e)?r[i]="string"==typeof n?"[content]":Ke(n,t+1):r[i]=Ke(n,t+1)}return r}return e}function Ze(e){return Ke(e)}var Xe,et,tt,rt,it,nt=E({"src/middleware/audit.ts"(){Be=new Set(["access_token","refresh_token","password","api_key","secret","token","authorization","credential","credentials","private_key"]),Je=new Set(["body","description","content","notes","summary","title","system_prompt","prompt"]),Qe=[/^[^\s@]+@[^\s@]+\.[^\s@]+$/,/^bearer\s+\S+$/i,/^(sk|pk|npm|gh|glpat|xoxb|xoxp|rk|SG\.)[-_][A-Za-z0-9_-]{16,}/,/^eyJ[A-Za-z0-9_-]+\.eyJ[A-Za-z0-9_-]+\.[A-Za-z0-9_-]+$/],Ge=200}}),at=E({"src/middleware/rate-limiter.ts"(){Xe=60,et=6e4}});function st(){const e=process.env.ATOMS_MCP_PROJECT_ID?.trim();return e?tt.test(e)?e:(rt||(process.stderr.write(`[atoms-mcp] WARNING: ATOMS_MCP_PROJECT_ID="${e.slice(0,50)}" is not a valid UUID — scope ignored.\n`),rt=!0),null):null}var ot,dt=E({"src/middleware/project-scope.ts"(){tt=/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i,rt=!1,it=class extends Error{expectedProjectId;receivedProjectId;constructor(e,t){super("Tool call rejected: project_id is outside the configured ATOMS_MCP_PROJECT_ID scope."),this.name="ProjectScopeError",this.expectedProjectId=e,this.receivedProjectId=t}}}});function ct(e){const t=function(e){return e.trim().toLowerCase().replace(/[^a-z0-9]+/g,"_").replace(/^_+|_+$/g,"")}(e??"");return t?t.includes("cursor")?"cursor":t.includes("copilot")?"copilot":t.includes("claude")?ot:t:ot}var lt,mt,pt,ut,_t,ft,ht=E({"src/core/client-identity.ts"(){ot="claude_desktop"}}),gt=E({"src/core/timestamps.ts"(){lt=o.z.string().datetime({offset:!0})}}),yt=E({"src/core/errors.ts"(){}}),wt={};function bt(e,t=pt){if("string"!=typeof e)return"";const r=e.replace(_t,"").replace(ft,"");return r.length<=t?r:r.slice(0,t)+"..."}function vt(e){return"string"!=typeof e?"":e.trim().toLowerCase().replace(/\s+/g,"-").replace(/[^a-z0-9-]/g,"").replace(/-+/g,"-").replace(/^-|-$/g,"")}function jt(e,t){return{status:"success",data:e,...t?{meta:t}:{}}}function St(e,t,r){return{total_count:e,limit:t,offset:r,has_more:r+t<e}}function xt(e,t){return{status:"error",message:e,next_steps:t}}function kt(e,t){return xt(`${e} '${bt(t)}' not found`,[`Verify the ${e.toLowerCase()} ID is correct`,"Use atoms_list_items or atoms_search to find valid IDs"])}function Et(e){return xt(`${e} role cannot modify project data`,["Contact your org admin to upgrade your role to editor","Use read-only tools (atoms_list_items, atoms_get_item, atoms_search) instead"])}function It(e){return xt(`Validation error: ${bt(e,ut)}`,["Check the parameter types and constraints in the tool description","Ensure all required parameters are provided"])}function At(){return xt("Not authenticated. 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r=a[e];r.includes(t)||r.push(t)},d=new Set([e.item_id]);for(const e of t)d.add(e.from_id),d.add(e.to_id);const c=n.data?.relationships??{};for(const e of Object.keys(a)){const t=c[e];if(Array.isArray(t))for(const e of t)"string"==typeof e&&d.add(e)}let l=new Set([e.item_id]);const m=Array.from(d);if(m.length>0){const{data:t,error:i}=await r.from("items").select("id").eq("project_id",e.project_id).is("deleted_at",null).in("id",m);if(i)throw new Error(i.message);l=new Set((t??[]).map(e=>e.id)),l.add(e.item_id)}const p=e=>l.has(e);for(const r of t)if(r.from_id===e.item_id){if(!p(r.to_id))continue;o(i[r.type]??r.type,r.to_id)}else{if(!p(r.from_id))continue;o(s[r.type]??r.type,r.from_id)}for(const t of Object.keys(a)){const r=c[t];if(Array.isArray(r))for(const i of r)"string"==typeof i&&i!==e.item_id&&p(i)&&o(t,i)}}let 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Lt(jt({id:n.id,type:n.type,title:Nt(n.title),summary:Nt(n.data?.summary),body:Nt(n.data?.body),tags:n.data?.tags??{domains:[]},ownership:n.data?.ownership??{primary:null,additional:[]},relationships:a,links:n.data?.links??[],fields:(t=n.data?.fields,!t||"object"!=typeof t||Array.isArray(t)?{}:Object.fromEntries(Object.entries(t).filter(e=>"string"==typeof e[1]).map(([e,t])=>[e,Nt(t)]))),status:n.data?.status,..."test-case"===n.type?{latest_result:s[0]?.result??"not-run",test_results:s}:{},metadata:{created_at:n.created_at,created_by:n.created_by,updated_at:n.updated_at,updated_by:n.updated_by,source_id:n.data?.metadata?.source_id}}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Ft(At()):Ft($t(e instanceof Error?e.message:String(e)))}var t}I(pr,{getItemHandler:()=>_r});var fr=E({"src/tools/get-item.ts"(){Ne(),nr(),Vt(),lr=["point","release_id","build","environment","tooling","step_results"]}}),hr={};async function gr(e){try{const t=await De();let r,i,n=null;try{n=await Kt(t,{baseline_id:e.baseline_id,project_id:e.project_id})}catch(e){return Ft($t(e.message))}if(n){const a=await er(t,e.project_id,n),s=e.query.trim().toLowerCase(),o=0===s.length?[]:a.filter(t=>{if(e.type&&t.type!==e.type)return!1;const r=t.data??{};return[t.title,r?.body,r?.summary].filter(e=>"string"==typeof e).map(e=>e.toLowerCase()).some(e=>e.includes(s))});i=o.length,r=o.slice(0,e.limit).map(e=>({id:e.id,title:e.title,type:e.type,data:e.data}))}else{const n=await tr(t,e.project_id,e.query,{type:e.type,limit:e.limit,asset:e.asset});r=n.items,i=n.totalCount}return Lt(jt(r.map(e=>({id:e.id,title:Nt(e.title),type:e.type,status:e.data?.status,domains:e.data?.tags?.domains??[],level:e.data?.tags?.level})),St(i,e.limit,0)))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Ft(At()):Ft($t(e instanceof Error?e.message:String(e)))}}I(hr,{searchHandler:()=>gr});var yr=E({"src/tools/search.ts"(){Ne(),nr(),Vt()}}),wr={};async function br(e){try{const t=await De(),{access_token:r}=await je(),{items:i,totalCount:n}=await async function(e,t,r,i){const{ATOMS_SUPABASE_URL:n,ATOMS_SUPABASE_ANON_KEY:a}=await Promise.resolve().then(()=>(we(),ge)),s=await fetch(`${n}/functions/v1/embed`,{method:"POST",headers:{"Content-Type":"application/json",Authorization:`Bearer ${i.accessToken}`,apikey:a},body:JSON.stringify({input:r})});if(!s.ok)throw new Error(`Embed function failed: ${s.status}`);const{embedding:o}=await s.json(),{data:d,error:c}=await e.rpc("semantic_search",{query_embedding:o,p_project_id:t,match_threshold:.3,match_count:i.limit,p_type:i.type||null});if(c)throw new Error(c.message);return{items:d??[],totalCount:(d??[]).length,method:"semantic"}}(t,e.project_id,e.query,{type:e.type,limit:e.limit,accessToken:r});return Lt(jt(i.map(e=>({id:e.id,title:Nt(e.title),type:e.type,status:e.data?.status,domains:e.data?.tags?.domains??[],level:e.data?.tags?.level})),St(n,e.limit,0)))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Ft(At()):Ft($t(e instanceof Error?e.message:String(e)))}}I(wr,{semanticSearchHandler:()=>br});var vr=E({"src/tools/semantic-search.ts"(){Ne(),Re(),nr(),Vt()}}),jr={};async function Sr(e){try{if(e.baseline_id&&e.as_of)return Ft(It("baseline_id and as_of are mutually exclusive"));const t=await De();let r;if(e.baseline_id){const i=await Zt(t,e.baseline_id);if(!i)return Ft(It(`Baseline ${e.baseline_id} not found`));if(i.project_id!==e.project_id)return Ft(It("Baseline does not belong to this project"));r=i.snapshot_at}else e.as_of&&(r=e.as_of);const{covered:i,uncovered:n,total:a}=await async function(e,t,r){let i,n,a;if(r.snapshotAt){const s=(await er(e,t,r.snapshotAt)).map(Xt);i=s.filter(e=>"requirement"===e.type),n=s.map(e=>({id:e.id,data:e.data})),a=[]}else{const{data:r,error:s}=await e.from("items").select("*").eq("project_id",t).eq("type","requirement").is("deleted_at",null);if(s)throw new 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Error&&e.message.includes("Not authenticated")?Ft(At()):Ft($t(e instanceof Error?e.message:String(e)))}}I(jr,{getCoverageHandler:()=>Sr});var xr,kr=E({"src/tools/get-coverage.ts"(){Ne(),nr(),Vt()}}),Er={};async function Ir(e){try{const t=await De();let r;if(e.release_id){const i=await Zt(t,e.release_id);if(!i)return Ft(It(`Release ${e.release_id} not found`));if(i.project_id!==e.project_id)return Ft(It("Release does not belong to this project"));if(null===i.release_version)return Ft(xt(`Baseline "${i.name}" is not a formal Release.`,["Promote the baseline to a Release first (Snapshots view in the app)","Use atoms_list_baselines to see which baselines carry a release_version"]));r=i}else{const{data:i,error:n}=await t.from("baselines").select("id, release_version, release_status").eq("project_id",e.project_id).eq("release_status","released").is("deleted_at",null).maybeSingle();if(n)return Ft($t(n.message));if(!i)return Ft(xr);r=i}const{data:i,error:n}=await t.rpc("verification_readiness",{p_project_id:e.project_id,p_release_id:r.id});if(n)return Ft(Mt(n));const{data:a,error:s}=await t.from("verification_status").select("requirement_id, state, stale, points_total, points_run").eq("project_id",e.project_id).eq("release_id",r.id);if(s)return Ft($t(s.message));const o=(a??[]).slice().sort((e,t)=>e.requirement_id<t.requirement_id?-1:e.requirement_id>t.requirement_id?1:0),d={release:{id:r.id,version:r.release_version,status:r.release_status},readiness:i??{},requirements:o,...0===o.length?{hint:"projection empty; an admin may need to run rebuild_verification_from_runs for this project"}:{}};if(e.include_gaps){const{data:i,error:n}=await t.rpc("verification_notrun_points",{p_project_id:e.project_id,p_release_id:r.id});if(n)return Ft(Mt(n));d.gaps=i??[]}return Lt(jt(d))}catch(e){return Ft(Mt(e))}}I(Er,{verificationStatusHandler:()=>Ir});var Ar=E({"src/tools/verification-status.ts"(){Ne(),nr(),Vt(),xr=xt("This project has no current formal 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Lt(jt(i,St(i.length,e.limit,0)))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Ft(At()):Ft($t(e instanceof Error?e.message:String(e)))}}I(Rr,{getHistoryHandler:()=>Or});var Dr=E({"src/tools/get-history.ts"(){Ne(),nr(),Vt()}});function zr(e){return`item_${e.replace(/[^A-Za-z0-9_]/g,"_")||"node"}`}function Hr(e){const t=Cr(`${e.id}: ${e.title}`);return"test-case"===e.type?`(["${t}"])`:"note"===e.type?`("${t}")`:`["${t}"]`}function Ur(e){const t=zr(e.from_id),r=zr(e.to_id);return"child"===e.type?`${t} --\x3e ${r}`:"verified_by"===e.type?`${t} -.-> ${r}`:"related"===e.type?`${t} -.- ${r}`:null}function Cr(e){return e.replace(/"/g,"'").replace(/[[\]{}()]/g,"").substring(0,70)}var qr=E({"src/core/mermaid.ts"(){}}),Tr={};async function Mr(e){try{if(e.baseline_id&&e.as_of)return Ft(It("baseline_id and as_of are mutually exclusive"));const t=await De();let r,i,n;if(e.baseline_id){const i=await Zt(t,e.baseline_id);if(!i)return Ft(It(`Baseline ${e.baseline_id} not 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n=S.default.createHmac("sha256",Si).update(r).digest("base64url"),a=Buffer.from(i,"utf8"),s=Buffer.from(n,"utf8");if(a.length!==s.length||!S.default.timingSafeEqual(a,s))return{valid:!1,reason:"Token signature invalid"};let o;try{o=JSON.parse(Buffer.from(r,"base64url").toString("utf8"))}catch{return{valid:!1,reason:"Token payload malformed"}}return"number"!=typeof o.exp||o.exp<Date.now()?{valid:!1,reason:"Token expired"}:o.tool!==t.tool?{valid:!1,reason:"Token issued for a different tool"}:o.project_id!==t.project_id?{valid:!1,reason:"Token issued for a different project"}:o.target!==t.target?{valid:!1,reason:"Token issued for a different target"}:{valid:!0}}function Ai(e){if(Array.isArray(e))return e.map(Ai);if(null!==e&&"object"==typeof e){const t={};for(const r of Object.keys(e).sort())t[r]=Ai(e[r]);return t}return e}function Ri(e){const t=JSON.stringify(Ai(e));return S.default.createHash("sha256").update(t).digest("base64url").slice(0,16)}var Oi,Di=E({"src/middleware/confirmation.ts"(){$(),ji=6e4,Si=(()=>{const e=process.env.ATOMS_MCP_CONFIRMATION_SECRET;return e&&e.length>=16?e:S.default.randomBytes(32).toString("base64url")})()}}),zi={};async function Hi(e){try{const t=await De(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Ft(Et("Viewer"));throw e}const i=await async function(e,t,r){const{data:i,error:n}=await e.from("items").select("*").eq("id",r).eq("project_id",t).maybeSingle();if(n)throw new Error(n.message);return i}(t,e.project_id,e.item_id);if(!i)return Ft(kt("Item",e.item_id));if(i.deleted_at)return Ft(It(`Item ${e.item_id} is already deleted`));if(ki(Oi)){const t={tool:Oi,project_id:e.project_id,target:e.item_id};if(!e.confirmation_token){const r=Ei(t);return Lt(jt({status:"confirmation_required",preview:{id:e.item_id,title:i.title,type:i.type,would_soft_delete:!0},confirmation_token:r.token,expires_at:r.expires_at,expires_in_seconds:r.expires_in_seconds,message:`Re-call atoms_delete_item with the same project_id, item_id, and confirmation_token within ${r.expires_in_seconds}s to execute.`}))}const r=Ii(e.confirmation_token,t);if(!r.valid)return Ft(It(`confirmation_token rejected: ${r.reason}`))}const{error:n}=await t.rpc("soft_delete_item_with_revision",{p_item_id:e.item_id,p_project_id:e.project_id,p_user_id:r,p_expected_updated_at:i.updated_at,p_event_source:"mcp",p_actor:Va(),p_session_id:Wa()});if(n)throw new Error(n.message);return Lt(jt({id:e.item_id,title:i.title,type:i.type,deleted:!0,message:`Item ${e.item_id} soft-deleted. It can still be found in audit logs.`}))}catch(e){return Ft(Mt(e))}}I(zi,{deleteItemHandler:()=>Hi});var Ui=E({"src/tools/delete-item.ts"(){Ne(),nr(),Ja(),Di(),Vt(),Oi="atoms_delete_item"}}),Ci={};async function qi(e){try{const t=await De(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Ft(Et("Viewer"));throw e}const{data:i,error:n}=await t.from("items").select("*").eq("id",e.item_id).eq("project_id",e.project_id).maybeSingle();if(n)throw new Error(n.message);if(!i)return Ft(kt("Item",e.item_id));if(!i.deleted_at)return Ft(xt(`Item ${e.item_id} is not deleted and cannot be restored.`,["Use atoms_get_item to view the current item state","Use atoms_delete_item first if you intended to delete it"]));const{error:a}=await t.rpc("save_item_with_revision",{p_item_id:e.item_id,p_project_id:e.project_id,p_type:i.type,p_title:i.title,p_data:i.data,p_user_id:r,p_event_source:"restore",p_event_session_id:Wa()??null,p_diff_summary:{changed_fields:["deleted_at"],restored:!0},p_expected_updated_at:i.updated_at});if(a)throw new Error(a.message);const{error:s}=await t.rpc("repair_live_item_relationships_from_jsonb",{p_project_id:e.project_id,p_item_id:e.item_id});if(s)throw new Error(`Relationship repair failed: ${s.message}`);return await t.from("change_history").insert({item_id:e.item_id,project_id:e.project_id,changed_by:r,event_type:"restored",old_data:null,new_data:i.data,actor:Va(),session_id:Wa()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),Lt(jt({id:e.item_id,title:i.title,type:i.type,restored:!0,message:`Item ${e.item_id} restored successfully.`}))}catch(e){return Ft(Mt(e))}}I(Ci,{restoreItemHandler:()=>qi});var Ti=E({"src/tools/restore-item.ts"(){Ne(),Ja(),Vt()}}),Mi={};async function Pi(e){try{const t=await De(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Ft(Et("Viewer"));throw e}const i=async(i,n,a)=>{const s=await Yt(t,e.project_id,i.from_id);if(!s)throw new Error(`Item "${i.from_id}" not found`);const o=await Yt(t,e.project_id,i.to_id);if(!o)throw new Error(`Item "${i.to_id}" not found`);const{error:d}=await t.rpc("apply_link_change",{p_project_id:e.project_id,p_from_id:i.from_id,p_to_id:i.to_id,p_type:i.type,p_action:i.action,p_user_id:r,p_event_source:"mcp",p_expected_from_updated_at:i.expected_from_updated_at??s.updated_at,p_expected_to_updated_at:i.expected_to_updated_at??o.updated_at});if(d)throw new Error(d.message);const c={item_id:i.from_id,project_id:e.project_id,changed_by:r,event_type:"updated",old_data:null,new_data:{relationship_change:{action:i.action,type:i.type,from:i.from_id,to:i.to_id}},actor:Va(),session_id:Wa()};n&&(c.batch_id=n),a&&(c.reason=a),await t.from("change_history").insert(c).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)})};if(e.operations&&Array.isArray(e.operations)){for(const t of e.operations)if(t.from_id===t.to_id)return Ft(It(`Self-reference in batch: "${t.from_id}"`));const r=[...new Set(e.operations.flatMap(e=>[e.from_id,e.to_id]))],{data:n}=await t.from("items").select("id").eq("project_id",e.project_id).is("deleted_at",null).in("id",r),a=new Set((n??[]).map(e=>e.id)),s=r.filter(e=>!a.has(e));if(s.length>0)return Ft(kt("Items",s.join(", ")));const{data:o}=await t.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id),d=new Map;for(const e of o??[])"parent"===e.type&&(d.has(e.from_id)||d.set(e.from_id,new Set),d.get(e.from_id).add(e.to_id));for(const t of e.operations){if("parent"!==t.type&&"child"!==t.type)continue;const[e,r]="parent"===t.type?[t.from_id,t.to_id]:[t.to_id,t.from_id];"remove"===t.action?d.get(e)?.delete(r):(d.has(e)||d.set(e,new Set),d.get(e).add(r))}const c=0,l=1,m=2,p=new Map,u=new Set;for(const[e,t]of d){u.add(e);for(const e of t)u.add(e)}const _=e=>{if((p.get(e)??c)!==c)return null;const t=[],r=[],i=e=>{p.set(e,l),r.push(e),t.push({node:e,parents:[...d.get(e)??[]],idx:0})};for(i(e);t.length>0;){const e=t[t.length-1];if(e.idx>=e.parents.length){p.set(e.node,m),r.pop(),t.pop();continue}const n=e.parents[e.idx];e.idx++;const a=p.get(n)??c;if(a===l){const e=r.indexOf(n);return[...r.slice(e),n]}a!==m&&i(n)}return null};for(const e of u){const t=_(e);if(t)return Ft(It(`Batch would create a cycle: ${t.join(" -> ")}. No changes applied.`))}const f=crypto.randomUUID(),h=e.operations.filter(e=>"remove"===e.action),g=e.operations.filter(e=>"add"===e.action);for(const t of[...h,...g])await i(t,f,e.reason);return Lt(jt({batch_id:f,processed:e.operations.length,operations:!1===e.echo?void 0:e.operations}))}return e.from_id&&e.to_id&&e.type&&e.action?e.from_id===e.to_id?Ft(It("Cannot create a relationship between an item and itself")):(await i({action:e.action,from_id:e.from_id,to_id:e.to_id,type:e.type,expected_from_updated_at:e.expected_from_updated_at,expected_to_updated_at:e.expected_to_updated_at},void 0,e.reason),!1===e.echo?Lt(jt({action:e.action,from_id:e.from_id,to_id:e.to_id})):Lt(jt({action:e.action,type:e.type,from_id:e.from_id,to_id:e.to_id,message:`Relationship ${"add"===e.action?"added":"removed"}: ${e.from_id} --[${e.type}]--\x3e ${e.to_id}`}))):Ft(It("Provide (from_id, to_id, type, action) for single-op or operations[] for batch."))}catch(e){return Ft(Mt(e))}}I(Mi,{linkItemsHandler:()=>Pi});var $i=E({"src/tools/link-items.ts"(){Ne(),nr(),Ja(),Vt()}}),Ni=E({"src/core/bulk-parent-links.ts"(){}}),Li={};function Fi(e){return new Set(["22023","23503","23505","23514"]).has(e.code??"")}async function Wi(e){try{if(!e.items||0===e.items.length)return Ft(It("items array must contain at least 1 item"));if(e.items.length>100)return Ft(It(`Maximum 100 items per call (received ${e.items.length}). Split into multiple calls.`));const t=await De(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Ft(Et("Viewer"));throw e}const i=await async function(e,t,r){const{data:i}=await e.from("metadata").select("domains").eq("project_id",t).maybeSingle(),n=i?.domains??[],a=n.length>0?new Set(n.map(vt).filter(e=>e.length>0)):null,s=Ri(n.map(vt).filter(e=>e.length>0).sort()),o=[],d=new Set,c={};for(let e=0;e<r.length;e++){const t=r[e];if(c[t.type]=(c[t.type]??0)+1,!a)continue;const i=(t.domains??[]).map(vt).filter(e=>e.length>0);if(0===i.length)continue;const s=i.filter(e=>!a.has(e));s.length>0&&(d.add(e),o.push({index:e,title:t.title,error:`Unknown domain${s.length>1?"s":""}: ${s.join(", ")}. 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Lt(jt({created:0,items:[],errors:o}));const m=[],p=new Map;for(const{itemId:t,input:i,sanitizedDomains:a,sanitizedLevel:s}of d){const o={id:t,type:i.type,title:i.title,summary:i.summary,body:i.body,tags:{domains:a,level:s??""},ownership:{primary:null,additional:[]},relationships:{parents:i.parent_id?[i.parent_id]:[],children:[],related:[]},links:[],metadata:{created_at:n,created_by:r,updated_at:n,updated_by:r}};p.set(t,o),m.push({id:t,project_id:e.project_id,type:i.type,title:i.title,data:o,created_by:r,updated_by:r})}const u=m.map(e=>({id:e.id,type:e.type,title:e.title,data:e.data})),{error:_}=await t.rpc("bulk_save_items_with_revisions",{p_project_id:e.project_id,p_items:u,p_user_id:r,p_event_source:"mcp"});if(_&&Fi(_))for(const{itemId:i,input:n,index:c}of d){const d=m.find(e=>e.id===i);if(!d)continue;const{error:l}=await t.rpc("save_item_with_revision",{p_item_id:d.id,p_project_id:e.project_id,p_type:d.type,p_title:d.title,p_data:d.data,p_user_id:r,p_event_source:"mcp",p_event_session_id:a,p_diff_summary:null});l?o.push({index:c,title:n.title,error:l.message}):s.push({id:i,title:n.title,type:n.type})}else{if(_)throw _;for(const{itemId:e,input:t}of d)s.push({id:e,title:t.title,type:t.type})}const f=d.filter(({input:e})=>e.parent_id).filter(({itemId:e})=>s.some(t=>t.id===e)).map(({itemId:t,input:r})=>({from_id:t,to_id:r.parent_id,type:"parent",project_id:e.project_id}));await async function(e){for(const t of e.links){const{error:r}=await e.client.rpc("apply_link_change",{p_project_id:e.projectId,p_from_id:t.from,p_to_id:t.to,p_type:"parent",p_action:"add",p_user_id:e.userId,p_event_source:"mcp"});r&&e.warn(`bulk parent link sync failed for ${t.to}: ${r.message??"unknown error"}`)}}({client:t,projectId:e.project_id,links:f.map(e=>({from:e.from_id,to:e.to_id})),userId:r,warn:e=>process.stderr.write(`[atoms-mcp] Warning: ${e}\n`)});const h=s.map(t=>({item_id:t.id,project_id:e.project_id,changed_by:r,event_type:"created",old_data:null,new_data:p.get(t.id)??null,actor:Va(),session_id:a}));h.length>0&&await t.from("change_history").insert(h).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: bulk change_history log failed: ${e.message}\n`)});const g=new Set(s.map(e=>e.id)),y=new Set(d.filter(({itemId:e,sanitizedLevel:t})=>t&&g.has(e)).map(({sanitizedLevel:e})=>e));for(const r of y)await Wr(t,e.project_id,r);return Lt(jt({created:s.length,items:s,errors:o.length>0?o:[],project_id:e.project_id}))}catch(e){return Ft(Mt(e))}}I(Li,{bulkImportHandler:()=>Wi,canRetryBulkImportPerItem:()=>Fi});var Vi=E({"src/tools/bulk-import.ts"(){Ne(),nr(),Ja(),Di(),Vt(),Ni(),Gr()}}),Bi={};async function Ji(e){try{const t=await De(),r=Ce(),i=qe();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Ft(Et("Viewer"));throw e}const n=await Yt(t,e.project_id,e.item_id);if(!n)return Ft(kt("Item",e.item_id));if("test-case"!==n.type)return Ft(It(`Item '${e.item_id}' is a ${n.type}, not a test-case`));const a=(e.asset??"").trim(),s=(new Date).toISOString(),{data:o,error:d}=await t.rpc("record_test_results_bulk",{p_project_id:e.project_id,p_item_id:e.item_id,p_run_by:i||r,p_actor_user_id:r,p_results:[{result:e.result,note:e.note,asset:a||void 0,date:s,point:e.point,release_id:e.release_id,build:e.build,environment:e.environment,tooling:e.tooling,steps_rev:e.steps_rev,step_results:e.step_results}]});if(d)throw new Error(d.message);const c=Array.isArray(o)?o[0]:o?.[0];await t.from("change_history").insert({item_id:e.item_id,project_id:e.project_id,changed_by:r,event_type:"test_result_recorded",old_data:null,new_data:{result:e.result,run_at:s,note:e.note,asset:a||null},actor:Va(),session_id:Wa()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)});const l=a?` (asset: ${a})`:"";return Lt(jt({item_id:e.item_id,result:e.result,run_at:s,run_by:i||r,note:e.note??null,asset:a||null,asset_id:c?.asset_id??null,asset_created:c?.asset_created??!1,message:`Test result '${e.result}' recorded for ${e.item_id}${l}`}))}catch(e){return Ft(Mt(e))}}I(Bi,{recordTestResultHandler:()=>Ji});var Qi=E({"src/tools/record-test-result.ts"(){Ne(),nr(),Ja(),Vt()}}),Gi={};async function Yi(e){try{const t=await De(),r=Ce(),i=qe();if(!Array.isArray(e.results)||0===e.results.length)return Ft(It("results must be a non-empty array"));if(e.results.length>100)return Ft(It(`results must have at most 100 entries (got ${e.results.length})`));try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Ft(Et("Viewer"));throw e}const n=await Yt(t,e.project_id,e.item_id);if(!n)return Ft(kt("Item",e.item_id));if("test-case"!==n.type)return Ft(It(`Item '${e.item_id}' is a ${n.type}, not a test-case`));const{data:a,error:s}=await t.rpc("record_test_results_bulk",{p_project_id:e.project_id,p_item_id:e.item_id,p_run_by:i||r,p_actor_user_id:r,p_results:e.results});if(s)throw new Error(s.message);return t.from("change_history").insert({item_id:e.item_id,project_id:e.project_id,changed_by:r,event_type:"test_result_recorded",old_data:null,new_data:{bulk:!0,count:e.results.length,results:a},actor:Va(),session_id:Wa()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),Lt(jt({item_id:e.item_id,count:e.results.length,results:a,message:`Recorded ${e.results.length} test results for ${e.item_id}`}))}catch(e){return Ft(Mt(e))}}I(Gi,{recordTestResultsBulkHandler:()=>Yi});var Ki,Zi,Xi,en,tn=E({"src/tools/record-test-results-bulk.ts"(){Ne(),nr(),Ja(),Vt()}});function rn(e){return Math.min(Math.max(e??5,1),10)}var nn=E({"src/core/trace-graph.ts"(){Ki=200,Zi=new Set(["parent","verifies","mitigated_by"]),Xi=new Set(["child","verified_by","mitigates"]),en={parent:"child",child:"parent",verifies:"verified_by",verified_by:"verifies",mitigated_by:"mitigates",mitigates:"mitigated_by",related:"related"}}}),an={};async function sn(e){try{const t=rn(e.depth),r=await De(),i=await Yt(r,e.project_id,e.item_id);if(!i)return Ft(kt("Item",e.item_id));const{data:n,error:a}=await r.from("items").select("id, title, type, data").eq("project_id",e.project_id).is("deleted_at",null);if(a)throw new Error(a.message);const{data:s,error:o}=await r.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(o)throw new Error(o.message);const d=rr(n??[],s??[]);return Lt(jt(function(e){const t=rn(e.depth),r=e.relationshipTypes?.length?new Set(e.relationshipTypes):null,i=new Map(e.items.map(e=>[e.id,e]));i.has(e.rootItemId)||i.set(e.rootItemId,e.rootItem);const n=new Map,a=(e,t,r)=>{n.has(e)||n.set(e,[]),n.get(e).push({neighbor:t,relType:r})};for(const t of e.relationships){const i=t.type;if(("upstream"===e.direction||"both"===e.direction)&&(!Zi.has(i)||r&&!r.has(i)||a(t.from_id,t.to_id,i),Xi.has(i))){const e=en[i]??i;r&&!r.has(e)||a(t.to_id,t.from_id,e)}if(("downstream"===e.direction||"both"===e.direction)&&(!Xi.has(i)||r&&!r.has(i)||a(t.from_id,t.to_id,i),Zi.has(i))){const e=en[i]??i;r&&!r.has(e)||a(t.to_id,t.from_id,e)}"related"!==i||r&&!r.has("related")||(a(t.from_id,t.to_id,"related"),a(t.to_id,t.from_id,"related"))}const s=new Set([e.rootItemId]),o=[],d=[],c=[];for(const t of n.get(e.rootItemId)??[])c.push({id:t.neighbor,depth:1,relType:t.relType,from:e.rootItemId});for(;c.length>0&&o.length<Ki;){const{id:e,depth:r,relType:a,from:l}=c.shift();if(s.has(e)||r>t)continue;s.add(e);const m=i.get(e);if(m&&(o.push({id:e,title:m.title,type:m.type,relationship:a,depth:r,from:l}),d.push({from:l,to:e,type:a}),r<t))for(const t of n.get(e)??[])s.has(t.neighbor)||c.push({id:t.neighbor,depth:r+1,relType:t.relType,from:e})}const l={id:e.rootItemId,title:e.rootItem.title,type:e.rootItem.type,relationship:"root",depth:0,from:e.rootItemId};return{root:e.rootItemId,project_id:e.projectId,direction:e.direction,depth_limit:t,items:[l,...o],edges:d,total_count:o.length+1,...o.length>=Ki?{truncated:!0,truncation_message:`Results capped at ${Ki} items. 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Call again with dry_run=false to apply.`}));let m;m=o?i.map(e=>e===a?s:e):i.includes(s)?i:[...i,s],await Sn(t,e.project_id,m,n);const{error:p}=await t.rpc("apply_domain_change",{p_project_id:e.project_id,p_old_domain:a,p_new_domain:s,p_user_id:r,p_event_source:"mcp"});if(p)throw new Error(p.message);return Lt(jt({domain:{name:s},renamed_from:a,items_updated:l,message:`Domain renamed "${a}" → "${s}". ${l} item${1!==l?"s":""} updated.`}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Ft(At()):Ft($t(e instanceof Error?e.message:String(e)))}}async function In(e){try{const t=await De(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Ft(Et("Viewer"));throw e}const{domains:i,levels:n}=await jn(t,e.project_id),a=e.name.trim().toLowerCase(),s=i.includes(a),{data:o,error:d}=await t.from("items").select("id, data").eq("project_id",e.project_id).is("deleted_at",null).filter("data->tags->domains","cs",JSON.stringify([a]));if(d)throw new Error(d.message);const c=(o??[]).length;if(!s&&0===c)return Ft(kt("Domain",a));if(c>0&&!e.force)return Ft(It(`Domain "${a}" is used by ${c} item${c>1?"s":""}. Use force=true to delete and strip the domain from all items, or re-tag them first.`));if(ki("atoms_delete_domain")){const t={tool:"atoms_delete_domain",project_id:e.project_id,target:a};if(!e.confirmation_token){const e=Ei(t);return Lt(jt({status:"confirmation_required",preview:{domain_name:a,items_using_count:c,would_strip_from_items:c>0},confirmation_token:e.token,expires_at:e.expires_at,expires_in_seconds:e.expires_in_seconds,message:`Re-call atoms_delete_domain with the same project_id, name, and confirmation_token within ${e.expires_in_seconds}s to execute.`}))}const r=Ii(e.confirmation_token,t);if(!r.valid)return Ft(It(`confirmation_token rejected: ${r.reason}`))}const l=s?i.filter(e=>e!==a):i;if(await Sn(t,e.project_id,l,n),c>0){const{error:i}=await t.rpc("apply_domain_change",{p_project_id:e.project_id,p_old_domain:a,p_new_domain:null,p_user_id:r,p_event_source:"mcp"});if(i)throw new Error(i.message)}return Lt(jt({deleted:!0,name:a,items_updated:c,message:c>0?`Domain "${a}" 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t=e.data?.tags?.domains??[];m.push({id:e.id,domains:t})}else"test-case"===e.type?(c.test_cases++,l.push(e.id)):"note"===e.type&&c.notes++;const p={passed:0,failed:0,blocked:0,not_run:0};if(l.length>0){const{data:r,error:i}=await t.from("test_results").select("item_id, result, run_at").eq("project_id",e.project_id).order("run_at",{ascending:!1});if(i)throw new Error(i.message);const n=new Map;for(const e of r??[])n.has(e.item_id)||n.set(e.item_id,e.result);for(const e of l){const t=n.get(e);t&&"not-run"!==t?"passed"===t?p.passed++:"failed"===t?p.failed++:"blocked"===t?p.blocked++:p.not_run++:p.not_run++}}const{data:u,error:_}=await t.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(_)throw new Error(_.message);const f=rr(s??[],u??[]),h=new Set;for(const e of f)"verifies"===e.type?h.add(e.to_id):"verified_by"===e.type&&h.add(e.from_id);const g=m.filter(e=>h.has(e.id)).length,y=m.length,w={covered:g,uncovered:y-g,total:y,percent:y>0?Math.round(g/y*1e3)/10:100},b=new Map;for(const e of m){const t=e.domains.length>0?e.domains:["(untagged)"],r=h.has(e.id);for(const e of t){b.has(e)||b.set(e,{covered:0,total:0});const t=b.get(e);t.total++,r&&t.covered++}}const v=Array.from(b.entries()).sort((e,t)=>e[0].localeCompare(t[0])).map(([e,t])=>({domain:e,covered:t.covered,total:t.total,percent:t.total>0?Math.round(t.covered/t.total*1e3)/10:100})),j=new Date;j.setDate(j.getDate()-7);const{count:S,error:x}=await t.from("change_history").select("id",{count:"exact",head:!0}).eq("project_id",e.project_id).gte("changed_at",j.toISOString());if(x)throw new Error(x.message);return Lt(jt({project_id:e.project_id,project_name:n??`Project ${e.project_id.slice(0,8)}`,counts:c,test_status:p,coverage:w,coverage_by_domain:v,recent_changes:S??0,last_updated:(new Date).toISOString()}))}catch(e){return e instanceof Error&&e.message.includes("Not 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a=n.get(t.variable_id)??t.variable_id;u.push({item_id:r,title:Nt(i.title),type:i.type,depth:1,relationship_path:[{from_id:e.item_id,to_id:r,relationship_type:`variable_ref:${a}`}]}),h++}}}const g={};for(const e of u)g[e.type]=(g[e.type]??0)+1;const y=c.get(e.item_id);return Lt(jt({root:{item_id:e.item_id,title:Nt(y?.title??n.title),type:y?.type??n.type},impacted_items:u,summary:{total_impacted:u.length,by_type:g,max_depth_reached:_,...h>0?{variable_impact_count:h}:{},...u.length>=Cn?{truncated:!0}:{}}}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Ft(At()):Ft($t(e instanceof Error?e.message:String(e)))}}I($n,{impactAnalysisHandler:()=>Nn});var Ln=E({"src/tools/impact-analysis.ts"(){Ne(),nr(),Vt(),Cn=200,qn=["parent","verifies","traces_to","allocated_from","decomposed_from"],Tn=["child","verified_by","allocated_to","decomposes_to","traced_by"],Mn={parent:"child",child:"parent",verifies:"verified_by",verified_by:"verifies",related:"related",traces_to:"traced_by",traced_by:"traces_to",allocated_to:"allocated_from",allocated_from:"allocated_to",decomposes_to:"decomposed_from",decomposed_from:"decomposes_to"}}}),Fn=E({"src/core/relationship-sync.ts"(){}}),Wn={};function Vn(e){return e instanceof Error&&e.message.includes("Not authenticated")?Ft(At()):null}async function Bn(e,t){const{data:r,error:i}=await e.rpc("restore_baseline_state",{p_baseline_id:t.baselineId,p_project_id:t.projectId,p_items:[],p_variables:[],p_user_id:t.userId});if(i)throw new Error(i.message);return r}async function Jn(e,t,r){const{data:i,error:n}=await e.from("items").select("id, deleted_at").eq("project_id",t).eq("id",r).maybeSingle();if(n)throw new 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n?"23505"===n.code?Ft(xt(`Baseline name "${e.name}" already exists in this project`,["Pick a different name"])):Ft($t(n.message)):Lt(jt({id:i.id,name:i.name,description:i.description,field_definitions_snapshot:i.field_definitions_snapshot,snapshot_at:i.snapshot_at,created_at:i.created_at,locked:!1}))}catch(e){return Vn(e)??Ft($t(e instanceof Error?e.message:String(e)))}}async function Kn(e){try{const t=await De(),r=await Zt(t,e.baseline_id);if(!r)return Ft(kt("Baseline",e.baseline_id));const i=await Qn(t,r.project_id,"baselines_enabled");if(i)return i;if(null!==r.locked_at)return Ft(xt("Baseline is already locked",["Locks are one-way; nothing to do"]));const{data:n}=await t.from("projects").select("org_id").eq("id",r.project_id).maybeSingle();if(!n)return Ft(kt("Project",r.project_id));const{data:a}=await t.auth.getUser(),s=a?.user?.id;if(!s)return Ft(At());const{data:o}=await t.from("org_members").select("role").eq("user_id",s).eq("org_id",n.org_id).maybeSingle();if(!o||"admin"!==o.role)return Ft(xt("Only admins can lock baselines",["Ask an org admin to lock this baseline"]));const{data:d,error:c}=await t.from("baselines").update({locked_at:(new Date).toISOString(),locked_by:s}).eq("id",e.baseline_id).select().single();return c?Ft($t(c.message)):Lt(jt({id:d.id,locked_at:d.locked_at,locked_by:d.locked_by}))}catch(e){return Vn(e)??Ft($t(e instanceof Error?e.message:String(e)))}}async function Zn(e){try{const t=await De(),[r,i]=await Promise.all([Zt(t,e.baseline_a_id),Zt(t,e.baseline_b_id)]);if(!r||!i)return Ft(kt("Baseline","one of the baseline_ids"));if(r.project_id!==i.project_id)return Ft(xt("Both baselines must belong to the same project",["Verify both baseline_ids are from the same project_id"]));const[n,a]=await Promise.all([er(t,r.project_id,r.snapshot_at),er(t,i.project_id,i.snapshot_at)]),s=new Map(n.map(e=>[e.id,e])),o=new Map(a.map(e=>[e.id,e])),d=Array.from(new Set([...s.keys(),...o.keys()])).sort(),c=[];let l=0,m=0,p=0;for(const e of d){const t=s.get(e),r=o.get(e);if(!t&&r)l++,c.push({item_id:e,change_type:"added"});else if(t&&!r)m++,c.push({item_id:e,change_type:"removed"});else if(t&&r){const i=[];t.title!==r.title&&i.push("title"),t.type!==r.type&&i.push("type");JSON.stringify(t.data??{})!==JSON.stringify(r.data??{})&&i.push("data"),i.length>0&&(p++,c.push({item_id:e,change_type:"modified",fields_changed:i}))}}const u=Math.max(e.offset??0,0),_=Math.min(Math.max(e.limit??50,1),200),f=e.detail?c.slice(u,u+_):c.slice(u,u+_).map(({item_id:e,change_type:t,fields_changed:r})=>({item_id:e,change_type:t,fields_changed:r}));return Lt(jt({summary:{added:l,removed:m,modified:p,total_compared:d.length},items:f,page_info:{offset:u,limit:_,total:c.length},baselines:{a:{id:r.id,name:r.name,snapshot_at:r.snapshot_at},b:{id:i.id,name:i.name,snapshot_at:i.snapshot_at}}}))}catch(e){return Vn(e)??Ft($t(e instanceof Error?e.message:String(e)))}}async function Xn(e){try{const t=await De(),r=await Zt(t,e.baseline_id);if(!r)return Ft(kt("Baseline",e.baseline_id));const i=await Qn(t,r.project_id,"baselines_enabled");if(i)return i;const{data:n}=await t.from("projects").select("org_id").eq("id",r.project_id).maybeSingle();if(!n)return Ft(kt("Project",r.project_id));const{data:a}=await t.auth.getUser(),s=a?.user?.id;if(!s)return Ft(At());const{data:o}=await t.from("org_members").select("role").eq("user_id",s).eq("org_id",n.org_id).maybeSingle();if(!o||"admin"!==o.role)return Ft(xt("Only admins can restore from a baseline",["Ask an org admin to run the restore"]));const{data:d}=await t.rpc("cc_project_is_controlled",{p_project_id:r.project_id});if(!0===d)return Ft(xt("Change control is on for this project. 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Lt(jt({preview:!0,items_to_restore:u.length,variables_to_restore:h.length,field_definitions_to_restore:r.field_definitions_snapshot?.length??null}));const g=await Bn(t,{baselineId:r.id,projectId:r.project_id,userId:s});return Lt(jt({ok:!0,items_restored:g.items_restored,variables_restored:g.variables_restored,field_definitions_restored:g.field_definitions.length}))}catch(e){return Vn(e)??Ft($t(e instanceof Error?e.message:String(e)))}}I(Wn,{createBaselineHandler:()=>Yn,diffBaselinesHandler:()=>Zn,listBaselinesHandler:()=>Gn,lockBaselineHandler:()=>Kn,restoreBaselineHandler:()=>Xn,restoreBaselineStateAtomically:()=>Bn,syncRestoredItemRelationships:()=>Jn});var ea,ta,ra,ia,na,aa,sa,oa,da,ca,la=E({"src/tools/baselines.ts"(){Ne(),Ja(),Vt(),nr(),Fn()}});function ma(e){const t=e?.severity||"",r=e?.exposure||"",i=e?.controllability||"";return t&&r&&i?"S0"===t||"E0"===r||"C0"===i?"QM":ra[`${t}-${r}-${i}`]||ea:ea}function pa(e){const t=parseInt(e?.severity||"",10),r=parseInt(e?.occurrence||"",10),i=parseInt(e?.detection||"",10);return Number.isNaN(t)||Number.isNaN(r)||Number.isNaN(i)?ea:String(t*r*i)}function ua(e,t){return"hara"===e?ma(t):pa(t)}function _a(e,t,r){if(r)return!1;if("hara"===e){const e=ma(t);return"C"===e||"D"===e}const i=parseInt(pa(t),10);return!Number.isNaN(i)&&i>=200}function fa(e,t,r){if(!e?.approved||!e.approved_at)return!1;const i=Date.parse(e.approved_at);return!Number.isNaN(i)&&[...e.source_req?[e.source_req]:[],...t].some(e=>{const t=r(e),n=t?Date.parse(t):NaN;return!Number.isNaN(n)&&n>i})}var ha,ga,ya=E({"src/core/analysis.ts"(){ea="—",ta=["prevention","detection","mitigation"],ra={"S1-E1-C1":"QM","S1-E1-C2":"QM","S1-E1-C3":"QM","S1-E2-C1":"QM","S1-E2-C2":"QM","S1-E2-C3":"QM","S1-E3-C1":"QM","S1-E3-C2":"QM","S1-E3-C3":"A","S1-E4-C1":"QM","S1-E4-C2":"A","S1-E4-C3":"B","S2-E1-C1":"QM","S2-E1-C2":"QM","S2-E1-C3":"QM","S2-E2-C1":"QM","S2-E2-C2":"QM","S2-E2-C3":"A","S2-E3-C1":"QM","S2-E3-C2":"A","S2-E3-C3":"B","S2-E4-C1":"A","S2-E4-C2":"B","S2-E4-C3":"C","S3-E1-C1":"QM","S3-E1-C2":"QM","S3-E1-C3":"A","S3-E2-C1":"QM","S3-E2-C2":"A","S3-E2-C3":"B","S3-E3-C1":"A","S3-E3-C2":"B","S3-E3-C3":"C","S3-E4-C1":"B","S3-E4-C2":"C","S3-E4-C3":"D"},na={hara:{severity:["S0","S1","S2","S3"],exposure:["E0","E1","E2","E3","E4"],controllability:["C0","C1","C2","C3"]},dfmea:{severity:ia=["1","2","3","4","5","6","7","8","9","10"],occurrence:ia,detection:ia}},aa={hara:["failure_mode","operating_scenario","severity","exposure","controllability","safe_state","ftti","rationale"],dfmea:["failure_mode","cause","severity","occurrence","detection","rationale"]},sa={hara:"safety-goal",dfmea:"failure-mode"},oa={hara:"SG",dfmea:"FM"},da={hara:"HARA",dfmea:"DFMEA"},ca={hara:"hara_iso26262",dfmea:"dfmea_rpn"}}}),wa={};function ba(e){return"safety-goal"===e?"hara":"failure-mode"===e?"dfmea":null}async function va(e,t,r){const{data:i,error:n}=await e.rpc("next_item_id",{p_project_id:t,p_prefix:r});if(n)throw new Error(`ID generation failed: ${n.message}`);return i}function ja(e){const t=e?.relationships?.mitigated_by;return Array.isArray(t)?t.filter(e=>"string"==typeof e):[]}function Sa(e){return JSON.parse(JSON.stringify(e??{}))}async function xa(e){try{const t=await De(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Ft(Et("Viewer"));throw e}const i=e.source_req_ids??[];if(i.length>50)return Ft(It("source_req_ids supports at most 50 entries per call"));if(i.length>0){const{data:r,error:n}=await t.from("items").select("id, type, data").eq("project_id",e.project_id).is("deleted_at",null).in("id",i);if(n)throw new Error(n.message);const a=new Map((r??[]).map(e=>[e.id,e])),s=i.filter(e=>!a.has(e));if(s.length>0)return Ft(kt("Source requirement(s)",s.join(", 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va(t,e.project_id,oa[n]),o={id:i,type:"requirement",title:"",body:"",req_type:d,tags:{domains:[],level:""},ownership:{primary:null,additional:[]},relationships:{parents:[a],children:[],related:[],verifies:[],verified_by:[]},links:[],analysis_props:{source_req:s,approved:!1,approved_at:null,field_source:{}},metadata:{created_at:c,created_by:r,updated_at:c,updated_by:r}},{error:l}=await t.rpc("save_item_with_revision",{p_item_id:i,p_project_id:e.project_id,p_type:"requirement",p_title:"",p_data:o,p_user_id:r,p_event_source:"mcp",p_event_session_id:Wa()??null,p_diff_summary:null});if(l)throw new Error(l.message);const{error:m}=await t.rpc("apply_link_change",{p_project_id:e.project_id,p_from_id:i,p_to_id:a,p_type:"parent",p_action:"add",p_user_id:r,p_event_source:"mcp"});m&&(process.stderr.write(`[atoms-mcp] Warning: analysis row parent link sync failed for ${i}: ${m.message}\n`),u.push({row_id:i,source_req:s,message:m.message})),await t.from("change_history").insert({item_id:i,project_id:e.project_id,changed_by:r,event_type:"created",old_data:null,new_data:o,actor:Va(),session_id:Wa()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),p.push({id:i,source_req:s})}return await t.from("change_history").insert({item_id:a,project_id:e.project_id,changed_by:r,event_type:"created",old_data:null,new_data:l,actor:Va(),session_id:Wa()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),Lt(jt({id:a,subtype:n,title:Nt(s),revision:o,rows:p,...u.length>0?{link_warnings:u,warning:`${u.length} row(s) were created but could not be attached to the analysis and will not appear in atoms_get_analysis. Repair: for each row in link_warnings, call atoms_link_items with type 'parent', from_id=<row id>, to_id=${a}.`}:{}}))}catch(e){return Ft(Mt(e))}}async function ka(e){try{const t=await De(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Ft(Et("Viewer"));throw e}const i=await Yt(t,e.project_id,e.row_id);if(!i)return Ft(kt("Analysis row",e.row_id));const n=i.data,a=ba(n?.req_type);if(!a)return Ft(It(`Item ${e.row_id} is not an analysis row (req_type must be 'safety-goal' or 'failure-mode')`));const s=new Set([...aa[a],"effect"]);"hara"===a&&s.add("title");const o=Object.keys(e.fields??{});if(0===o.length)return Ft(It("fields must contain at least one key"));const d=o.filter(e=>!s.has(e));if(d.length>0)return Ft(It(`Unknown field(s) for ${a}: ${d.join(", ")}. Allowed: ${[...s].sort().join(", ")}`));const c=na[a],l={};for(const t of o){const r=e.fields[t];if(c[t]){const e="number"==typeof r&&"dfmea"===a?String(r):r;if("string"!=typeof e||!c[t].includes(e))return Ft(It(`Invalid ${t} value ${JSON.stringify(r)} for ${a}. Allowed: ${c[t].join(", ")}`));l[t]=e}else{if("string"!=typeof r)return Ft(It(`Field '${t}' must be a string`));l[t]=r}}const m=n?.analysis_props??null,p=Sa(n);p.analysis_props&&"object"==typeof p.analysis_props||(p.analysis_props={source_req:null,approved:!1,approved_at:null,field_source:{}});const u=p.analysis_props;u.field_source&&"object"==typeof u.field_source||(u.field_source={});let _=i.title;for(const[e,t]of Object.entries(l))"effect"===e?p.body=t:"title"===e?(p.title=t,_=t):(u[e]=t,"failure_mode"===e&&"dfmea"===a&&(p.title=t,_=t)),u.field_source[e]="mcp";const f=(new Date).toISOString();p.metadata={...p.metadata??{},updated_at:f,updated_by:r};const{data:h,error:g}=await t.rpc("save_item_with_revision",{p_item_id:i.id,p_project_id:e.project_id,p_type:i.type,p_title:_,p_data:p,p_user_id:r,p_event_source:"mcp",p_event_session_id:Wa()??null,p_diff_summary:null,p_expected_updated_at:i.updated_at});if(g)throw new Error(g.message);if(!h)return Ft(xt(`Fill silently failed for '${e.row_id}': save RPC returned no row. Likely RLS denied the write.`,["Verify you have editor or admin role in this project","Retry after checking project access"]));await t.from("change_history").insert({item_id:i.id,project_id:e.project_id,changed_by:r,event_type:"updated",old_data:n,new_data:p,actor:Va(),session_id:Wa()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)});const y=ua(a,u),w=[];if("hara"===a){const n=ua("hara",m),a=ja(p);if(a.length>0&&y!==ea&&y!==n)for(const n of a){const a=await Yt(t,e.project_id,n);if(!a)continue;const s=a.data;if(s?.asil===y&&s?.asil_source===i.id)continue;const o=s?.asil??null,d=s?.asil_source??null,c=Sa(s);c.asil=y,c.asil_source=i.id,c.metadata={...c.metadata??{},updated_at:f,updated_by:r};const{error:l}=await t.rpc("save_item_with_revision",{p_item_id:a.id,p_project_id:e.project_id,p_type:a.type,p_title:a.title,p_data:c,p_user_id:r,p_event_source:"mcp",p_event_session_id:Wa()??null,p_diff_summary:null,p_expected_updated_at:a.updated_at});if(l)throw new Error(l.message);await t.from("change_history").insert({item_id:a.id,project_id:e.project_id,changed_by:r,event_type:"updated",old_data:{asil:o,asil_source:d},new_data:{asil:y,asil_source:i.id},actor:Va(),session_id:Wa(),reason:`ASIL propagated from ${i.id} (rating change via atoms_fill_row)`}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),w.push(n)}}return Lt(jt({row_id:i.id,subtype:a,written_fields:Object.keys(l),computed_level:y,...w.length>0?{asil_propagated_to:w}:{}}))}catch(e){return Ft(Mt(e))}}async function Ea(e,t,r){const i=await Yt(e,t,r);if(!i)return{ok:!1,result:Ft(kt("Analysis",r))};if("analysis"!==i.type)return{ok:!1,result:Ft(It(`Item ${r} is not an analysis (type='${i.type}')`))};const n=i.data,a=ba("hara"===n?.analysis?.subtype?"safety-goal":"dfmea"===n?.analysis?.subtype?"failure-mode":null);if(!a)return{ok:!1,result:Ft(It(`Analysis ${r} is missing a valid analysis.subtype`))};const s=sa[a],o=Array.isArray(n?.relationships?.children)?n.relationships.children.filter(e=>"string"==typeof e):[];let d=[];if(o.length>0){const{data:r,error:i}=await e.from("items").select("*").eq("project_id",t).is("deleted_at",null).in("id",o);if(i)throw new Error(i.message);const n=new Map((r??[]).filter(e=>!e.deleted_at&&o.includes(e.id)&&e.data?.req_type===s).map(e=>[e.id,e]));d=o.map(e=>n.get(e)).filter(e=>Boolean(e))}const c=new Set;for(const e of d){const t=e.data?.analysis_props??{};"string"==typeof t.source_req&&t.source_req&&c.add(t.source_req);for(const t of ja(e.data))c.add(t)}const l=new Map;if(c.size>0){const{data:r,error:i}=await e.from("items").select("id, updated_at").eq("project_id",t).is("deleted_at",null).in("id",[...c]);if(i)throw new Error(i.message);for(const e of r??[])l.set(e.id,e.updated_at)}const m=d.map(e=>{const t=e.data?.analysis_props??{},r=ja(e.data).filter(e=>l.has(e)),i=r.length>0,n=ua(a,t),s=function(e,t,r){if(r)return null;if("hara"===e){const e=ma(t);return"QM"!==e&&e!==ea?`asil ${e} unmitigated`:null}const i=parseInt(pa(t),10),n=parseInt(t?.severity||"",10);return!Number.isNaN(i)&&i>=100?"rpn >= 100":!Number.isNaN(n)&&n>=9?"severity >= 9":null}(a,t,i),o={id:e.id,title:Nt("string"==typeof e.title?e.title:""),source_req:"string"==typeof t.source_req?t.source_req:null,effect:Nt("string"==typeof e.data?.body?e.data.body:""),computed_level:n,is_gap:null!==s,gap_rule:s,is_critical:_a(a,t,i),is_stale:fa(t,r,e=>l.get(e)??null),mitigated_by:r,link_roles:t.link_roles??{},approved:!0===t.approved,approved_at:t.approved_at??null,mcp_fields:Object.entries(t.field_source??{}).filter(([,e])=>"mcp"===e).map(([e])=>e).sort()};for(const e of aa[a]){const r=t[e]??null;o[e]=ga.has(e)&&"string"==typeof r?Nt(r):r}return o});return{ok:!0,analysis:{id:i.id,title:Nt("string"==typeof i.title?i.title:""),subtype:a,scheme:"string"==typeof n?.analysis?.scheme?n.analysis.scheme:ca[a],revision:"string"==typeof n?.analysis?.revision?n.analysis.revision:"1.0"},rows:m,counts:{rows:m.length,gaps:m.filter(e=>e.is_gap).length,critical:m.filter(e=>e.is_critical).length,stale:m.filter(e=>e.is_stale).length,approved:m.filter(e=>e.approved).length,linked:m.filter(e=>e.mitigated_by.length>0).length}}}async function Ia(e){try{const t=await De(),r=await Ea(t,e.project_id,e.analysis_id);return r.ok?Lt(jt({analysis:r.analysis,rows:r.rows,counts:r.counts})):r.result}catch(e){return Ft(Mt(e))}}async function Aa(e){try{const n=await De(),a=Ce();try{await Te(n,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Ft(Et("Viewer"));throw e}if(e.row_id===e.req_id)return Ft(It("row_id and req_id must be different items"));const s=await Yt(n,e.project_id,e.row_id);if(!s)return Ft(kt("Analysis row",e.row_id));const o=s.data,d=ba(o?.req_type);if(!d)return Ft(It(`Item ${e.row_id} is not an analysis row (req_type must be 'safety-goal' or 'failure-mode')`));const c=await Yt(n,e.project_id,e.req_id);if(!c)return Ft(kt("Requirement",e.req_id));const l=c.data;if("requirement"!==c.type||ha.has(l?.req_type))return Ft(It(`req_id must reference a plain requirement (type='requirement', not an analysis row): ${e.req_id}`));if("dfmea"===d&&!e.role)return Ft(It(`role is required for dfmea mitigation links. Choose one of: ${ta.join(", ")}`));if("hara"===d&&e.role)return Ft(It("role is not applicable to hara mitigation links; omit it (roles are a dfmea concept)"));let m=ea;if("hara"===d){m=ua("hara",o?.analysis_props);const n=l?.asil;if(m!==ea&&"string"==typeof n&&n.length>0&&n!==m&&!0!==e.override)return Ft((r=m,{...xt(`ASIL conflict: the target requirement already carries asil '${t=n}' but ${i=s.id} computes '${r}'.`,["Pass override=true to apply the HARA value; the override is history-logged like a dialog accept","Or align the row's S/E/C ratings with the existing ASIL before linking"]),details:{code:"asil_conflict",current_value:t,incoming_value:r,source_row:i,hint:"pass override=true to apply the HARA value; the override is history-logged like a dialog accept"}}))}const p="dfmea"===d?e.role:null,{error:u}=await n.rpc("apply_link_change",{p_project_id:e.project_id,p_from_id:e.row_id,p_to_id:e.req_id,p_type:"mitigated_by",p_action:"add",p_user_id:a,p_event_source:"mcp",p_expected_from_updated_at:s.updated_at,p_expected_to_updated_at:c.updated_at,p_role:p});if(u)throw new Error(u.message);let _;if(await n.from("change_history").insert({item_id:e.row_id,project_id:e.project_id,changed_by:a,event_type:"updated",old_data:null,new_data:{relationship_change:{action:"add",type:"mitigated_by",from:e.row_id,to:e.req_id,...p?{role:p}:{}}},actor:Va(),session_id:Wa()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),"hara"===d&&m!==ea){const t=await Yt(n,e.project_id,e.req_id);if(t){const r=t.data,i=r?.asil??null,o=r?.asil_source??null,d=Sa(r);d.asil=m,d.asil_source=s.id;const c=(new Date).toISOString();d.metadata={...d.metadata??{},updated_at:c,updated_by:a};const{error:l}=await n.rpc("save_item_with_revision",{p_item_id:t.id,p_project_id:e.project_id,p_type:t.type,p_title:t.title,p_data:d,p_user_id:a,p_event_source:"mcp",p_event_session_id:Wa()??null,p_diff_summary:null,p_expected_updated_at:t.updated_at});if(l)throw new Error(l.message);await n.from("change_history").insert({item_id:t.id,project_id:e.project_id,changed_by:a,event_type:"updated",old_data:{asil:i,asil_source:o},new_data:{asil:m,asil_source:s.id},actor:Va(),session_id:Wa(),reason:!0===e.override?`ASIL override accepted via atoms_link_mitigation (was '${i??"unset"}', now '${m}' from ${s.id})`:`ASIL set via atoms_link_mitigation from ${s.id}`}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),_=m}}return Lt(jt({row_id:e.row_id,req_id:e.req_id,type:"mitigated_by",role:p,..._?{asil_written:_}:{}}))}catch(e){return Ft(Mt(e))}var t,r,i}async function Ra(e){try{const t=await De(),r=await Ea(t,e.project_id,e.analysis_id);if(!r.ok)return r.result;const i=r.rows.filter(e=>e.is_gap).map(e=>({id:e.id,title:e.title,source_req:e.source_req,computed_level:e.computed_level,rule:e.gap_rule}));return Lt(jt({analysis_id:r.analysis.id,subtype:r.analysis.subtype,gaps:i,count:i.length}))}catch(e){return Ft(Mt(e))}}I(wa,{createAnalysisHandler:()=>xa,fillRowHandler:()=>ka,getAnalysisHandler:()=>Ia,getGapsHandler:()=>Ra,linkMitigationHandler:()=>Aa});var Oa,Da,za,Ha,Ua,Ca,qa,Ta,Ma,Pa,$a=E({"src/tools/analysis.ts"(){Ne(),nr(),Ja(),Vt(),ya(),ha=new Set(["safety-goal","failure-mode"]),ga=new Set(["failure_mode","cause","operating_scenario","safe_state","ftti","rationale"])}}),Na={};function La(e){F(e.toolName)&&function(e,t){const r=`ui://${t.toolName}/${t.htmlFile}`,i=function(e,t){const r=s.fileURLToPath("undefined"==typeof document?require("url").pathToFileURL(__filename).href:p&&"SCRIPT"===p.tagName.toUpperCase()&&p.src||new URL("index.cjs",document.baseURI).href),i=j.default.dirname(r);return j.default.resolve(i,"apps","src","apps",e,t)}(t.appName,t.htmlFile),n=[...Wt.resourceDomains,...t.extraResourceDomains??[]];d.registerAppTool(e,t.toolName,{title:t.title,description:t.description,inputSchema:t.inputSchema,annotations:t.annotations,_meta:{ui:{resourceUri:r}}},t.handler),d.registerAppResource(e,`${t.title} UI`,r,{mimeType:d.RESOURCE_MIME_TYPE},async()=>{const e=await v.default.readFile(i,"utf-8");return{contents:[{uri:r,mimeType:d.RESOURCE_MIME_TYPE,text:e,_meta:{ui:{csp:{resourceDomains:n}}}}]}})}(Ha,e)}function Fa(e,t){return async r=>{const i=O(P(),e);if(!i.allowed)return Ft(xt(`Tool ${e} is blocked by org policy.`,[z(i.reason),"Contact your org admin to adjust the MCP access policy."]));try{!function(e){const t=st();if(!t)return;if("object"!=typeof e||null===e)return;const r=e.project_id;if("string"==typeof r&&r!==t)throw new it(t,r)}(r)}catch(e){if(e instanceof it)return Ft(Ot(e.expectedProjectId));throw e}{const e=P(),t=r?.project_id;if(null!==e.project_scope&&"string"==typeof t&&!e.project_scope.includes(t))return Ft(xt("Tool call rejected: project_id is outside your org's MCP project scope.",[`Allowed projects: ${e.project_scope.length} project${1===e.project_scope.length?"":"s"} configured by your admin`,"Use atoms_list_projects to see which projects you can access in this session"]))}let n,a;try{a=await De(),n=Ce()}catch{return t(r)}const s=await async function(e,t){const r=parseInt(process.env.ATOMS_RATE_LIMIT_RPM??"",10)||Xe,i=new Date,n=new Date(i.getTime()-et);try{const{count:a,error:s}=await t.from("mcp_rate_limits").select("id",{count:"exact",head:!0}).eq("user_id",e).gte("requested_at",n.toISOString());if(s)throw new Error(s.message);if((a??0)>=r){const{data:r,error:a}=await t.from("mcp_rate_limits").select("requested_at").eq("user_id",e).gte("requested_at",n.toISOString()).order("requested_at",{ascending:!0}).limit(1).maybeSingle();if(a)throw new Error(a.message);const s=(r?new Date(r.requested_at).getTime():i.getTime())+et-i.getTime();return{allowed:!1,retryAfterSeconds:Math.max(1,Math.ceil(s/1e3))}}t.from("mcp_rate_limits").insert({user_id:e,requested_at:i.toISOString()}).then(({error:e})=>{e&&process.stderr.write(`[rate-limiter] insert failed: ${e.message}\n`)});const o=new Date(i.getTime()-2*et);return t.from("mcp_rate_limits").delete().eq("user_id",e).lt("requested_at",o.toISOString()).then(()=>{}),{allowed:!0}}catch(e){return process.stderr.write(`[rate-limiter] DB check failed (${e instanceof Error?e.message:String(e)}), falling back to allow.\n`),{allowed:!0}}}(n,a);if(!s.allowed)return Ft(Dt(s.retryAfterSeconds));if("1"===process.env.ATOMS_MCP_LOCKDOWN||"true"===process.env.ATOMS_MCP_LOCKDOWN){const e=r?.project_id;if("string"==typeof e)try{const{requireWriteAccess:t}=await Promise.resolve().then(()=>(Ne(),Oe));await t(a,e)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message){const{accessDeniedError:e}=await Promise.resolve().then(()=>(Vt(),wt));return Ft(e("Viewer (lockdown mode: read access requires editor or admin)"))}}}const o=function(){const e=performance.now();return()=>Math.round(performance.now()-e)}();let d,c="success";try{const e=await t(r),i=e;if(!0===i?.isError){c="error";const e=i?.content;if(e?.[0]?.text)try{d=JSON.parse(e[0].text).message}catch{}}return e}catch(e){throw c="error",d=e instanceof Error?e.message:String(e),e}finally{const t={tool_name:e,params:r,status:c,duration_ms:o(),error_msg:d,project_id:r.project_id,session_id:Ca,client_name:qa};try{!function(e,t,r){const i=Ze(r.params);e.from("mcp_audit_log").insert({user_id:t,tool_name:r.tool_name,params:i,status:r.status,duration_ms:r.duration_ms,error_msg:r.error_msg??null,project_id:r.project_id??null,session_id:r.session_id??null,client_name:r.client_name??null}).then(({error:e})=>{e&&process.stderr.write(`[audit] Failed to log: ${e.message}\n`)})}(await De(),n,t)}catch{}}}}function Wa(){return Ca}function Va(){return Ta}function Ba(){return qa}I(Na,{ATOMS_MCP_SERVER_VERSION:()=>za,getMcpActor:()=>Va,getMcpClientName:()=>Ba,getMcpSessionId:()=>Wa,server:()=>Ha});var Ja=E({"src/server.ts"(){nt(),at(),B(),dt(),$(),T(),ht(),gt(),Ne(),Vt(),Bt(),Oa=l.createRequire("undefined"==typeof document?require("url").pathToFileURL(__filename).href:p&&"SCRIPT"===p.tagName.toUpperCase()&&p.src||new URL("index.cjs",document.baseURI).href),Da=Oa("../package.json"),za=Da.version,Ha=new c.McpServer({name:"atoms-mcp-server",version:za}),Ua=(e,t,r)=>{if(F(e))return Ha.registerTool(e,t,r)},Ca=a.randomUUID(),qa=ct(process.env.ATOMS_CLIENT_NAME),Ta=function(){const e=ct(qa);return"cursor"===e?"mcp_cursor":"copilot"===e?"mcp_copilot":"mcp_claude"}(),Ua("atoms_status",{title:"ATOMS MCP Health Check",description:'Check the health and authentication status of the ATOMS MCP server.\n\nCall this FIRST if other atoms tools fail or return auth errors.\nThis tool works WITHOUT authentication — it checks whether credentials\nexist and are valid, and tells the user exactly what to do if not.\n\nArgs: None\n\nReturns:\n { status: "authenticated"|"not_authenticated"|"expired", email, message, next_steps }\n\nExamples:\n - "Is ATOMS MCP working?" → atoms_status()\n - "Why are atoms tools failing?" → atoms_status()',inputSchema:{},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},async()=>{try{const{readCredentials:e,isTokenValid:t}=await Promise.resolve().then(()=>(oe(),J)),r=await e();if(!r)return{content:[{type:"text",text:JSON.stringify({status:"not_authenticated",message:"No ATOMS credentials found. You need to login first.",next_steps:["1. Open a terminal on your machine","2. Run: npx @atoms-tech/atoms-mcp login","3. Complete the login in your browser","4. Restart Claude Desktop (quit and reopen)","5. Try your query again"]},null,2)}]};if(!t(r))try{const{getValidToken:e}=await Promise.resolve().then(()=>(Re(),be)),{email:t}=await e(),{invalidateClient:r}=await Promise.resolve().then(()=>(Ne(),Oe));return r(),{content:[{type:"text",text:JSON.stringify({status:"authenticated",email:t,message:"Token was expired but has been refreshed. You're good to go!"},null,2)}]}}catch{return{content:[{type:"text",text:JSON.stringify({status:"expired",email:r.user_email??"unknown",message:"Your session has expired and could not be refreshed.",next_steps:["1. Open a terminal on your machine","2. Run: npx @atoms-tech/atoms-mcp logout","3. Run: npx @atoms-tech/atoms-mcp login","4. Complete the login in your browser","5. Restart Claude Desktop (quit and reopen)"]},null,2)}]}}return{content:[{type:"text",text:JSON.stringify({status:"authenticated",email:r.user_email??"unknown",message:"ATOMS MCP is connected and authenticated. All tools are ready."},null,2)}]}}catch(e){return{content:[{type:"text",text:JSON.stringify({status:"error",message:`Health check failed: ${e instanceof Error?e.message:String(e)}`,next_steps:["1. Open a terminal","2. Run: npx @atoms-tech/atoms-mcp login","3. Restart Claude Desktop"]},null,2)}]}}}),Ua("atoms_list_projects",{title:"List ATOMS Projects",description:'List all projects the authenticated user has access to.\n\nThis is the ENTRY POINT tool. Call this first to discover project IDs,\nthen use those IDs with all other tools.\n\nArgs: None\n\nReturns:\n { status: "success", data: [{ id, name, description, org_id, created_at }] }\n\nExamples:\n - "What projects do I have?" → atoms_list_projects()\n - "Show my projects" → atoms_list_projects()\n\nWorkflow:\n atoms_list_projects → atoms_list_items(project_id) → atoms_get_item(project_id, item_id)',inputSchema:{},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_list_projects",async()=>{const{listProjectsHandler:e}=await Promise.resolve().then(()=>(or(),ar));return e()})),Ua("atoms_list_items",{title:"List ATOMS Items",description:'List items in an ATOMS project with optional type/domain/level filters.\n\nThis is the primary ENTRY POINT for discovering items. Use it to browse\nproject contents before drilling into specific items with atoms_get_item.\n\nArgs:\n - project_id (string, UUID): The project to list items from\n - type (string, optional): Filter: requirement|test-case|note|table\n - domain (string, optional): Filter by domain tag\n - level (string, optional): Filter by level (System, Subsystem, Component)\n - limit (number, optional): Max results, 1-200 (default 50)\n - offset (number, optional): Pagination offset (default 0)\n\nReturns:\n { status: "success", data: [{ id, title, type, status, domains, level }], meta: { total_count, limit, offset, has_more } }\n\nExamples:\n - "Show me all requirements" → atoms_list_items(project_id, type="requirement")\n - "What test cases exist?" → atoms_list_items(project_id, type="test-case")\n\nErrors:\n - "Project not found" → verify project_id\n - "Access denied" → check org membership',inputSchema:{project_id:o.z.string().uuid("Must be a valid project UUID").describe("UUID of the project"),type:o.z.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),domain:o.z.string().max(64).optional().describe("Filter by domain tag (e.g., 'Safety', 'Performance')"),level:o.z.string().max(32).optional().describe("Filter by level (System, Subsystem, Component)"),limit:o.z.number().int().min(1).max(200).default(50).describe("Max results (default 50, max 200)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset (default 0)"),baseline_id:o.z.string().uuid().optional().describe("Optional baseline UUID. Returns items as they were at that baseline's moment. Mutually exclusive with as_of."),as_of:o.z.string().datetime().optional().describe("Optional ISO 8601 timestamp. Returns items as they were at that moment. Mutually exclusive with baseline_id.")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_list_items",async e=>{const{listItemsHandler:t}=await Promise.resolve().then(()=>(mr(),dr));return t(e)})),Ua("atoms_get_item",{title:"Get ATOMS Item Details",description:'Get full details of a single item including relationships, test history, and ownership.\n\nUse after atoms_list_items or atoms_search to drill into a specific item.\n\nArgs:\n - project_id (string, UUID): The project containing the item\n - item_id (string): Item ID (e.g., "REQ-001", "TC-050")\n\nReturns:\n Full WorkItem with relationships, test runs, ownership, metadata.\n\nExamples:\n - "Show me requirement REQ-001" → atoms_get_item(project_id, "REQ-001")\n - "Get test case details" → atoms_get_item(project_id, "TC-050")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID (e.g., REQ-001)"),baseline_id:o.z.string().uuid().optional().describe("Optional baseline UUID. Returns the item as it was at that baseline's moment. Mutually exclusive with as_of."),as_of:o.z.string().datetime().optional().describe("Optional ISO 8601 timestamp. Returns the item as it was at that moment. Mutually exclusive with baseline_id.")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_get_item",async e=>{const{getItemHandler:t}=await Promise.resolve().then(()=>(fr(),pr));return t(e)})),Ua("atoms_search",{title:"Search ATOMS Items",description:'Full-text search across items in a project. Searches title, body, and summary.\n\nAlternative entry point to atoms_list_items when you know what you\'re looking for.\n\nArgs:\n - project_id (string, UUID): The project to search in\n - query (string): Search text (max 1000 chars)\n - type (string, optional): Filter by type\n - asset (string, optional): Filter to items with at least one run on the given asset\n (VIN, module, lot, ...). Case-sensitive exact match.\n - limit (number, optional): Max results, 1-100 (default 25)\n\nReturns:\n Matching items with @basic fields, ranked by relevance.\n\nExamples:\n - "Find braking requirements" → atoms_search(project_id, "braking system")\n - "Search for safety tests" → atoms_search(project_id, "safety", type="test-case")\n - "Tests that ran on this VIN" → atoms_search(project_id, "", asset="WEV...0005")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),query:o.z.string().min(1).max(1e3).describe("Search text"),type:o.z.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),asset:o.z.string().max(200).optional().describe("Filter to items with at least one run on this asset (case-sensitive exact)"),limit:o.z.number().int().min(1).max(100).default(25).describe("Max results (default 25, max 100)"),baseline_id:o.z.string().uuid().optional().describe("Optional baseline UUID. Searches within the project state at that baseline's moment.")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_search",async e=>{const{searchHandler:t}=await Promise.resolve().then(()=>(yr(),hr));return t(e)})),Ua("atoms_semantic_search",{title:"Semantic Search ATOMS Items",description:'Meaning-based search across items using pgvector embeddings (GTE-small, 384d).\n\nUse when atoms_search (exact/substring) misses conceptually related items.\nBest for natural-language concept queries; atoms_search is better for exact phrases or IDs.\n\nArgs:\n - project_id (string, UUID): The project to search in\n - query (string): Natural-language concept query (max 1000 chars)\n - type (string, optional): Filter by type\n - limit (number, optional): Max results, 1-50 (default 10)\n\nReturns:\n Semantically similar items ranked by cosine similarity.\n\nExamples:\n - "Find braking-related requirements" → atoms_semantic_search(project_id, "braking deceleration stopping distance")\n - "Safety-related test cases" → atoms_semantic_search(project_id, "hazard risk mitigation safety", type="test-case")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),query:o.z.string().min(1).max(1e3).describe("Natural-language concept query"),type:o.z.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),limit:o.z.number().int().min(1).max(50).default(10).describe("Max results (default 10, max 50)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_semantic_search",async e=>{const{semanticSearchHandler:t}=await Promise.resolve().then(()=>(vr(),wr));return t(e)})),La({appName:"coverage",htmlFile:"coverage-app.html",toolName:"atoms_get_coverage",title:"Get Test Coverage Report",description:'Find requirements without linked test cases (coverage gaps).\n\nEssential for compliance reporting in safety-critical industries.\n\nIn MCP App hosts (Claude, ChatGPT), renders a visual coverage heatmap.\nFalls back to JSON for non-UI clients.\n\nArgs:\n - project_id (string, UUID): The project to analyze\n - domain (string, optional): Filter by domain\n - level (string, optional): Filter by level\n - baseline_id (string, UUID, optional): coverage at that baseline\'s moment\n - as_of (string ISO 8601, optional): coverage at that moment\n baseline_id and as_of are mutually exclusive.\n\nReturns:\n { covered, uncovered, total, coverage_percent, uncovered_items: [...] }\n\nExamples:\n - "What\'s our test coverage?" → atoms_get_coverage(project_id)\n - "Safety coverage gaps?" → atoms_get_coverage(project_id, domain="Safety")\n - "Coverage at PDR submission" → atoms_get_coverage(project_id, baseline_id="...")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),domain:o.z.string().max(64).optional().describe("Filter by domain tag"),level:o.z.string().max(32).optional().describe("Filter by level"),baseline_id:o.z.string().uuid().optional().describe("Compute coverage as of this baseline's snapshot moment"),as_of:o.z.string().datetime().optional().describe("Compute coverage as of this ISO 8601 moment")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Fa("atoms_get_coverage",async e=>{const{getCoverageHandler:t}=await Promise.resolve().then(()=>(kr(),jr));return t(e)})}),Ua("atoms_verification_status",{title:"Get Release Verification Status",description:'Release-bound verification state per requirement, matching the in-app projection.\n\nEach requirement\'s state is derived from the runs bound to a formal Release:\nverified, failing, incomplete, or not-run, plus a stale flag and the\n(points_run / points_total) counts for its parameterized test points.\n\nArgs:\n - project_id (string, UUID): The project to report on\n - release_id (string, UUID, optional): A formal Release (a baselines row with\n a release_version). Defaults to the project\'s CURRENT Release\n (release_status = \'released\'). Errors if the project has none.\n - include_gaps (boolean, optional, default false): Also return the not-run\n (test x unit x value) points for the Release.\n\nReturns:\n { release: {id, version, status}, readiness: {...roll-up counts...},\n requirements: [{requirement_id, state, stale, points_total, points_run}],\n gaps?: [{tc_id, asset, point_key}] }\n An empty requirements array with a "hint" field means the projection has not\n been rebuilt for this project yet, NOT that everything is unverified.\n\nExamples:\n - "Are we ready to ship 2.0?" → atoms_verification_status(project_id)\n - "What\'s still not run for release R?" → atoms_verification_status(project_id, release_id="...", include_gaps=true)',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),release_id:o.z.string().uuid().optional().describe("Formal Release (baselines row) UUID; defaults to the project's current Release"),include_gaps:o.z.boolean().default(!1).describe("Include the not-run (test x unit x value) points for the Release")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_verification_status",async e=>{const{verificationStatusHandler:t}=await Promise.resolve().then(()=>(Ar(),Er));return t(e)})),Ua("atoms_get_history",{title:"Get Item Change History",description:"Audit trail for an item — who changed what, when, and whether it was human or AI.\n\nShows actor attribution (user vs mcp_<client>) and session grouping.\n\nArgs:\n - project_id (string, UUID): The project containing the item\n - item_id (string): Item ID\n - limit (number, optional): Max entries (default 20, max 100)\n\nReturns:\n Change entries with actor, session_id, event_type, changed_at, fields_changed.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID"),limit:o.z.number().int().min(1).max(100).default(20).describe("Max entries (default 20)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_get_history",async e=>{const{getHistoryHandler:t}=await Promise.resolve().then(()=>(Dr(),Rr));return t(e)})),La({appName:"mermaid",htmlFile:"mermaid-app.html",toolName:"atoms_export_mermaid",title:"Export Mermaid Diagram",description:"Generate a Mermaid diagram of the requirement/test hierarchy.\n\nOutput is paste-ready for markdown docs. Shows parent-child relationships\nand requirement-to-test-case verification links.\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive pan/zoom diagram.\nFalls back to Mermaid text for non-UI clients.\n\nArgs:\n - project_id (string, UUID): The project to visualize\n - root_item_id (string, optional): Start node (default: all roots)\n - depth (number, optional): Max depth (default 3, max 10)\n - include_tests (boolean, optional): Show test case links (default true)\n - baseline_id (string, UUID, optional): render the graph at that baseline's moment\n - as_of (string ISO 8601, optional): render the graph at that moment\n baseline_id and as_of are mutually exclusive.\n\nReturns:\n Mermaid graph string.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),root_item_id:o.z.string().max(20).optional().describe("Root item ID to start from"),depth:o.z.number().int().min(1).max(10).default(3).describe("Max depth"),include_tests:o.z.boolean().default(!0).describe("Include test case links"),baseline_id:o.z.string().uuid().optional().describe("Render the graph as of this baseline's snapshot moment"),as_of:o.z.string().datetime().optional().describe("Render the graph as of this ISO 8601 moment")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Fa("atoms_export_mermaid",async e=>{const{exportMermaidHandler:t}=await Promise.resolve().then(()=>(Pr(),Tr));return t(e)})}),Ua("atoms_create_item",{title:"Create ATOMS Item",description:'Create a new requirement, test case, or note in a project.\n\nRequires editor or admin role. Changes are logged with AI actor attribution.\n\nArgs:\n - project_id (string, UUID): Target project\n - type (string): requirement|test-case|note\n - title (string): Item title (max 500 chars)\n - body (string, optional): Rich text body\n - summary (string, optional): Brief summary\n - domains (string[], optional): Domain tags\n - level (string, optional): System|Subsystem|Component\n - parent_ids (string[], optional): Parent item IDs to link\n - fields (object, optional): Project-field values, e.g. {"Verification Method": "Design Review"}. Keys must be defined via atoms_create_field first and values must match each field type.\n\nReturns:\n Created item with generated ID (e.g., "REQ-058")\n\nSide effects:\n - Logs to change_history with actor=\'mcp_<client>\'\n - Creates relationships if parent_ids provided',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the target project"),type:o.z.enum(["requirement","test-case","note"]).describe("Item type"),title:o.z.string().min(1).max(500).describe("Item title"),body:o.z.string().max(5e4).optional().describe("Rich text body"),summary:o.z.string().max(2e3).optional().describe("Brief summary"),domains:o.z.array(o.z.string().max(64)).max(20).optional().describe("Domain tags"),level:o.z.string().max(32).optional().describe("System|Subsystem|Component"),parent_ids:o.z.array(o.z.string().max(20)).max(50).optional().describe("Parent item IDs to link"),fields:o.z.record(o.z.string().max(60),o.z.string().max(1e4)).optional().describe("Project-field values keyed by defined field name"),echo:o.z.boolean().optional().describe("false → lean {id,type} response, saves ~580 tokens")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_create_item",async e=>{const{createItemHandler:t}=await Promise.resolve().then(()=>(hi(),_i));return t(e)})),Ma={steps:o.z.array(o.z.object({id:o.z.string().describe("Stable step id within the item"),instruction:o.z.string().describe("What the tester does"),test_data:o.z.string().optional().describe("Optional test data for the step"),expected:o.z.string().describe("Expected result")}).passthrough()).optional().describe("Test-case script steps: array of {id, instruction, test_data?, expected}. Max 50 steps, enforced by the DB trigger."),params:o.z.array(o.z.object({name:o.z.string().describe("Parameter name; steps reference it as {name}"),unit:o.z.string().optional().describe("Optional unit (e.g. km/h, V, m)"),values:o.z.array(o.z.union([o.z.string(),o.z.number()])).describe("Value set the test sweeps")}).passthrough()).optional().describe("Matrix parameters: array of {name, unit, values[]}. Matrix points (product of value-set sizes) capped at 64 by the DB trigger.")},Ua("atoms_update_item",{title:"Update ATOMS Item",description:'Update an existing item\'s fields. Only provided fields are changed.\n\nRequires editor or admin role. Logs old/new data diff to change history.\n\nArgs:\n - project_id (string, UUID): Project containing the item\n - item_id (string): Item to update\n - title, body, summary, domains, level, status: Fields to update (all optional)\n - fields (object, optional): Project-field values, e.g. {"Verification Method": "Design Review"}. Keys must be defined via atoms_create_field; merged per key, "" clears a key; non-empty values must match each field type\n - steps (array, optional): Test-case script steps [{id, instruction, test_data?, expected}]. Max 50 steps (DB-enforced)\n - params (array, optional): Matrix parameters [{name, unit, values[]}]. Matrix points capped at 64 (DB-enforced)\n - expected_updated_at (string, optional): Pass metadata.updated_at from atoms_get_item to reject stale writes\n\nReturns:\n Updated item.',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).optional().describe("Item ID (single form)"),title:o.z.string().min(1).max(500).optional().describe("New title"),body:o.z.string().max(5e4).optional().describe("New body"),summary:o.z.string().max(2e3).optional().describe("New summary"),domains:o.z.array(o.z.string().max(64)).max(20).optional().describe("New domain tags"),level:o.z.string().max(32).optional().describe("New level"),status:o.z.enum(["passed","failed","blocked","not-run"]).optional().describe("Test case status"),fields:o.z.record(o.z.string().max(60),o.z.string().max(1e4)).optional().describe('Project-field values keyed by defined field name; "" clears a key'),...Ma,expected_updated_at:lt.optional().describe("metadata.updated_at value from atoms_get_item; rejects stale writes"),echo:o.z.boolean().optional().describe("false → lean {id,updated_fields} response, saves ~580 tokens"),reason:o.z.string().max(500).optional().describe("Change rationale, persisted in audit history"),updates:o.z.array(o.z.object({item_id:o.z.string().min(1).max(20),title:o.z.string().min(1).max(500).optional(),body:o.z.string().max(5e4).optional(),summary:o.z.string().max(2e3).optional(),domains:o.z.array(o.z.string().max(64)).max(20).optional(),level:o.z.string().max(32).optional(),status:o.z.enum(["passed","failed","blocked","not-run"]).optional(),fields:o.z.record(o.z.string().max(60),o.z.string().max(1e4)).optional(),...Ma,expected_updated_at:lt.optional()})).optional().describe("Array form: update many items in one call"),idempotency_key:o.z.string().max(128).optional().describe("Safe retry key (24h TTL)"),continue_on_error:o.z.boolean().optional().describe("Allow partial success (default false = atomic)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_update_item",async e=>{const{updateItemHandler:t}=await Promise.resolve().then(()=>(xi(),bi));return t(e)})),Ua("atoms_delete_item",{title:"Delete ATOMS Item",description:'Soft-delete an item (sets deleted_at, preserves for audit trail).\n\nRequires editor or admin role. The item is never truly removed.\n\nWhen ATOMS_MCP_REQUIRE_CONFIRMATION is set on the server, this tool uses a\ntwo-step flow: the first call returns a preview + confirmation_token; the\nsecond call (with the token) executes. Tokens expire in 60s and are bound\nto (tool, project_id, item_id).\n\nArgs:\n - project_id (string, UUID): Project containing the item\n - item_id (string): Item to delete\n - confirmation_token (string, optional): Token from a prior preview call\n\nReturns:\n Confirmation with deleted item summary, or { status: "confirmation_required",\n preview, confirmation_token } when the confirmation gate is active.',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID to soft-delete"),confirmation_token:o.z.string().max(500).optional().describe("Token from a prior preview call (only used when ATOMS_MCP_REQUIRE_CONFIRMATION is set)")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_delete_item",async e=>{const{deleteItemHandler:t}=await Promise.resolve().then(()=>(Ui(),zi));return t(e)})),Ua("atoms_restore_item",{title:"Restore ATOMS Item",description:'Undo a soft-delete — restores an item that was previously deleted with atoms_delete_item.\n\nOnly works on items that have been soft-deleted (still in the database with deleted_at set).\nHas no effect if the item is not deleted. Logs the restoration to change_history.\n\nArgs:\n - project_id (string, UUID): Project containing the item\n - item_id (string): ID of the deleted item to restore\n\nReturns:\n Confirmation with the restored item\'s title and type.\n\nExamples:\n - "Restore the deleted requirement REQ-042" → atoms_restore_item(project_id, "REQ-042")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().max(256).describe("ID of the soft-deleted item to restore")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_restore_item",async e=>{const{restoreItemHandler:t}=await Promise.resolve().then(()=>(Ti(),Ci));return t(e)})),Ua("atoms_link_items",{title:"Link ATOMS Items",description:"Add or remove relationships between items.\n\nSupports: parent, child, related, verifies, verified_by.\nUpdates both items' JSONB data and the shadow table.\n\nArgs:\n - project_id (string, UUID): Project containing both items\n - from_id (string): Source item\n - to_id (string): Target item\n - type (string): parent|child|related|verifies|verified_by\n - action (string): add|remove\n - expected_from_updated_at / expected_to_updated_at (string, optional): pass metadata.updated_at values from atoms_get_item to reject stale link commands\n\nReturns:\n Updated relationship state for both items.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),from_id:o.z.string().min(1).max(20).optional().describe("Source item ID (single form)"),to_id:o.z.string().min(1).max(20).optional().describe("Target item ID (single form)"),type:o.z.enum(["parent","child","related","verifies","verified_by"]).optional().describe("Relationship type"),action:o.z.enum(["add","remove"]).optional().describe("Add or remove"),expected_from_updated_at:lt.optional().describe("metadata.updated_at for from_id from atoms_get_item"),expected_to_updated_at:lt.optional().describe("metadata.updated_at for to_id from atoms_get_item"),echo:o.z.boolean().optional().describe("false → lean response"),reason:o.z.string().max(500).optional().describe("Change rationale, persisted in audit history"),operations:o.z.array(o.z.object({action:o.z.enum(["add","remove"]),from_id:o.z.string().min(1).max(20),to_id:o.z.string().min(1).max(20),type:o.z.enum(["parent","child","related","verifies","verified_by"]),expected_from_updated_at:lt.optional(),expected_to_updated_at:lt.optional()})).optional().describe("Array form: batch relationship ops. Always atomic with DAG cycle detection."),idempotency_key:o.z.string().max(128).optional().describe("Safe retry key (24h TTL)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_link_items",async e=>{const{linkItemsHandler:t}=await Promise.resolve().then(()=>($i(),Mi));return t(e)})),La({appName:"import",htmlFile:"import-app.html",toolName:"atoms_bulk_import",title:"Bulk Import ATOMS Items",description:"Bulk create multiple items in a single tool call. Essential for AI agents\nthat generate 20+ requirements at once.\n\nChecks write access once, generates sequential IDs, batch inserts all items,\nand reports per-item errors without aborting the entire batch.\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive results table.\nFalls back to JSON for non-UI clients.\n\nArgs:\n - project_id (string, UUID): Target project\n - items (array): Up to 100 items to create, each with:\n - type (string): requirement|test-case|note\n - title (string): Item title (max 500 chars)\n - body (string, optional): Rich text body\n - summary (string, optional): Brief summary\n - domains (string[], optional): Domain tags\n - level (string, optional): System|Subsystem|Component\n - parent_id (string, optional): Parent item ID to link\n\nReturns:\n { created: number, items: [{ id, title, type }], errors: [] }\n\nLimits:\n - Maximum 100 items per call\n - If any item fails, others still succeed — errors reported separately\n\nSide effects:\n - Logs to change_history with actor='mcp_<client>' for each created item\n - Creates parent relationships for items with parent_id",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the target project"),items:o.z.array(o.z.object({type:o.z.enum(["requirement","test-case","note"]).describe("Item type"),title:o.z.string().min(1).max(500).describe("Item title"),body:o.z.string().max(5e4).optional().describe("Rich text body"),summary:o.z.string().max(2e3).optional().describe("Brief summary"),domains:o.z.array(o.z.string().max(64)).max(20).optional().describe("Domain tags"),level:o.z.string().max(32).optional().describe("System|Subsystem|Component"),parent_id:o.z.string().max(20).optional().describe("Parent item ID to link")})).min(1).max(100).describe("Items to create (1-100)"),confirmation_token:o.z.string().max(500).optional().describe("Token from a prior preview call (only used when ATOMS_MCP_REQUIRE_CONFIRMATION is set)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1},handler:Fa("atoms_bulk_import",async e=>{const{bulkImportHandler:t}=await Promise.resolve().then(()=>(Vi(),Li));return t(e)})}),Pa={point:o.z.record(o.z.string(),o.z.union([o.z.string(),o.z.number()])).optional().describe('Matrix point this run executed, e.g. {"speed": 40}'),release_id:o.z.string().uuid().optional().describe("Formal Release to bind this run to (a baseline with a release_version)"),build:o.z.string().optional().describe("Free-text build label"),environment:o.z.string().optional().describe("Structured environment field, distinct from build"),tooling:o.z.string().optional().describe("Structured tooling field, distinct from build"),steps_rev:o.z.string().optional().describe("Item revision id the run's steps were pinned to"),step_results:o.z.array(o.z.object({step_id:o.z.string().describe("Step id from data.steps"),status:o.z.enum(["passed","failed","blocked","skipped"]).describe("Per-step status"),actual:o.z.string().optional().describe("Actual-result note"),evidence_url:o.z.string().optional().describe("Evidence URL (validated server-side)")}).passthrough()).optional().describe("Per-step results [{step_id, status, actual?, evidence_url?}]. When present the run verdict is derived server-side and the top-level result is ignored.")},Ua("atoms_record_test_result",{title:"Record Test Result",description:"Record a pass/fail/blocked result for a test case.\n\nAppends to canonical items.data.runs and projects test_results from that\nhistory. Use atoms_get_item to see all results.\n\nArgs:\n - project_id (string, UUID): Project containing the test case\n - item_id (string): Test case ID (e.g., \"TC-001\")\n - result (string): passed|failed|blocked|not-run\n - note (string, optional): Reason or comment for this result\n - asset (string, optional): Asset identifier this run was executed against\n (VIN, module ID, lot number, serial number, etc). Max 200 chars.\n Auto-trimmed; empty/whitespace is treated as omitted. If the asset\n name does not yet exist in the project, it is auto-registered.\n - point, release_id, build, environment, tooling, steps_rev (optional):\n run metadata. release_id must be a formal Release (a baseline with a\n release_version). All validated server-side.\n - step_results (array, optional): per-step outcomes for a stepped run.\n When provided, the verdict is derived server-side from the steps.\n\nReturns:\n Recorded result with timestamp. When asset is provided, also returns\n asset_id and asset_created.\n\nSide effects:\n - Appends to items.data.runs through save_item_with_revision\n - Projects public.test_results from items.data.runs\n - Inserts into assets table if asset name is new in this project\n - Logs to change_history with actor='mcp_<client>'",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Test case ID (e.g., TC-001)"),result:o.z.enum(["passed","failed","blocked","not-run"]).describe("Test result"),note:o.z.string().max(500).optional().describe("Reason or comment for this result"),asset:o.z.string().max(200).optional().describe("Asset identifier this run was executed against (VIN, module ID, lot, etc). Auto-registered if new."),...Pa},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_record_test_result",async e=>{const{recordTestResultHandler:t}=await Promise.resolve().then(()=>(Qi(),Bi));return t(e)})),Ua("atoms_record_test_results",{title:"Record Test Results (bulk)",description:'Record many runs on one test case in a single atomic call.\n\nOptimized for multi-asset campaigns. Each entry can have its own asset and\nresult. Asset lookup-or-create happens per entry; new asset names are\nauto-registered. Runs are appended to canonical items.data.runs, then\ntest_results is projected from that history. The whole call is one DB\ntransaction; any entry failure rolls back the rest.\n\nUse the singular atoms_record_test_result for one-off runs.\n\nArgs:\n - project_id (string, UUID): Project containing the test case\n - item_id (string): Test case ID (e.g., "TC-001")\n - results (array, 1-100 entries): Each entry has:\n - asset (string, optional): Asset identifier (VIN, module ID, lot)\n - result (string, required): passed|failed|blocked|not-run\n - note (string, optional): Run note\n - date (string, optional): ISO 8601 datetime, default now()\n - point, release_id, build, environment, tooling, steps_rev (optional):\n run metadata; release_id must be a formal Release. Server-validated.\n - step_results (array, optional): per-step outcomes; when present the\n verdict is derived server-side from the steps.\n\nReturns:\n Per-entry outcomes with asset_id, asset_created, run_at, ok flags.\n\nSide effects:\n - Appends to items.data.runs through save_item_with_revision\n - Projects public.test_results from items.data.runs\n - Inserts new rows into assets for any asset name not already registered\n - Logs a single change_history entry summarizing the batch',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Test case ID (e.g., TC-001)"),results:o.z.array(o.z.object({asset:o.z.string().max(200).optional().describe("Asset identifier this run was executed against. Auto-registered if new."),result:o.z.enum(["passed","failed","blocked","not-run"]).describe("Test result"),note:o.z.string().max(500).optional().describe("Run note"),date:o.z.string().optional().describe("ISO 8601 datetime (default: now())"),...Pa})).min(1).max(100).describe("1 to 100 result entries on this test case")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_record_test_results",async e=>{const{recordTestResultsBulkHandler:t}=await Promise.resolve().then(()=>(tn(),Gi));return t(e)})),La({appName:"trace",htmlFile:"trace-app.html",toolName:"atoms_trace",title:"Trace Item Relationships",description:'Walk the traceability graph from a starting item.\n\nAnswers questions like "which requirements does TC-003 verify?" or\n"if I change REQ-001, what\'s affected downstream?"\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive graph visualization.\nFalls back to flat list for non-UI clients.\n\nArgs:\n - project_id (string, UUID): Project containing the item\n - item_id (string): Starting item ID\n - direction (string): upstream|downstream|both\n - upstream: follow parent/verifies links (dependencies)\n - downstream: follow child/verified_by links (dependents)\n - both: trace in both directions\n - depth (number, optional): Max traversal depth (default 5, max 10)\n - relationship_types (string[], optional): Filter to specific types (parent, child, related, verifies, verified_by, mitigated_by, mitigates)\n\nReturns:\n { root, direction, items: [{ id, title, type, relationship, depth }], total_count }\n\nExamples:\n - "What does TC-003 verify?" → atoms_trace(project_id, "TC-003", "upstream")\n - "What\'s affected by REQ-001?" → atoms_trace(project_id, "REQ-001", "downstream")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Starting item ID"),direction:o.z.enum(["upstream","downstream","both"]).describe("Traversal direction"),depth:o.z.number().int().min(1).max(10).default(5).describe("Max traversal depth (default 5)"),relationship_types:o.z.array(o.z.enum(["parent","child","related","verifies","verified_by","mitigated_by","mitigates"])).optional().describe("Filter to specific relationship types")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Fa("atoms_trace",async e=>{const{traceHandler:t}=await Promise.resolve().then(()=>(on(),an));return t(e)})}),Ua("atoms_list_assets",{title:"List Project Assets",description:"List asset identifiers registered in a project.\n\nAssets are free-form per-instance IDs (VINs, module names, lot numbers,\nserial numbers) that test runs are tagged against. They are auto-registered\nthe first time they appear on a run via atoms_record_test_result.\n\nArgs:\n - project_id (string, UUID): Project to list assets for\n - include_archived (boolean, optional): Include archived assets (default false)\n\nReturns:\n { assets: [{ id, name, archived_at, created_at }], total }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),include_archived:o.z.boolean().optional().describe("Include archived assets (default false)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_list_assets",async e=>{const{listAssetsHandler:t}=await Promise.resolve().then(()=>(ln(),dn));return t(e)})),Ua("atoms_list_variables",{title:"List Project Variables",description:"List all parameterized variables defined in a project.\n\nVariables are shared values (e.g., backup_camera_latency = 2s) that can be\nreferenced in requirement bodies as {variable_name}.\n\nArgs:\n - project_id (string, UUID): Project to list variables for\n - baseline_id (string, UUID, optional): list variables as they were at that baseline\n - as_of (string ISO 8601, optional): list variables as they were at that moment\n - limit (number, optional): max results (default 50, max 200)\n - offset (number, optional): pagination offset (default 0)\n\nReturns:\n { variables: [{ id, name, value, unit, description }], total }, meta: { total_count, limit, offset, has_more }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),baseline_id:o.z.string().uuid().optional().describe("Optional baseline UUID for time-travel reads"),as_of:o.z.string().datetime().optional().describe("Optional ISO timestamp for time-travel reads"),limit:o.z.number().int().min(1).max(200).default(50).describe("Max results (default 50, max 200)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset (default 0)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_list_variables",async e=>{const{listVariablesHandler:t}=await Promise.resolve().then(()=>(bn(),mn));return t(e)})),Ua("atoms_get_variable",{title:"Get Project Variable",description:'Get a specific variable by name, including which items reference it.\n\nArgs:\n - project_id (string, UUID): Project containing the variable\n - variable_name (string): Variable name (e.g., "backup_camera_latency")\n - baseline_id (string, UUID, optional): get the variable as it was at that baseline\n - as_of (string ISO 8601, optional): get the variable as it was at that moment\n\nReturns:\n { variable, referenced_by: [{ id, title, type }], reference_count }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),variable_name:o.z.string().min(1).max(64).describe("Variable name"),baseline_id:o.z.string().uuid().optional().describe("Optional baseline UUID for time-travel reads"),as_of:o.z.string().datetime().optional().describe("Optional ISO timestamp for time-travel reads")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_get_variable",async e=>{const{getVariableHandler:t}=await Promise.resolve().then(()=>(bn(),mn));return t(e)})),Ua("atoms_update_variable",{title:"Update Project Variable",description:"Update a variable's value, unit, or description.\n\nArgs:\n - project_id (string, UUID): Project containing the variable\n - variable_name (string): Variable name\n - value (string, optional): New value\n - unit (string, optional): Unit abbreviation (e.g., 's', 'Hz')\n - description (string, optional): Human-readable description\n\nReturns:\n { variable }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),variable_name:o.z.string().min(1).max(64).describe("Variable name"),value:o.z.string().max(500).optional().describe("New value"),unit:o.z.string().max(32).optional().describe("Unit abbreviation"),description:o.z.string().max(2e3).optional().describe("Description")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_update_variable",async e=>{const{updateVariableHandler:t}=await Promise.resolve().then(()=>(bn(),mn));return t(e)})),Ua("atoms_create_variable",{title:"Create Project Variable",description:'Create one or many parameterized variables for a project.\n\nSingle form: provide name + value.\nArray form: provide variables[] for bulk creation (one atomic INSERT).\n\nVariables can then be embedded in requirement bodies as {variable_name}.\n\nArgs (single form):\n - project_id (string, UUID): Project to add the variable to\n - name (string): Variable name, letters, digits, underscores; must start with letter/underscore\n - value (string): Initial value (e.g., "100", "true", "nominal")\n - unit (string, optional): Unit abbreviation (e.g., "Hz", "ms", "m/s²")\n - description (string, optional): Human-readable description\n - echo (bool, optional): false → lean {name} response (default true)\n\nArgs (array form):\n - project_id (string, UUID): Project UUID\n - variables[]: Array of { name, value, unit?, description? }\n - echo (bool, optional): false → lean {name} list (default true)\n - idempotency_key (string, optional): Dedup key\n\nReturns (single): { variable, message }\nReturns (array): { batch_id, created, variables, message }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).optional().describe("Variable name (single form)"),value:o.z.string().min(1).max(500).optional().describe("Initial value (single form)"),unit:o.z.string().max(32).optional().describe("Unit abbreviation"),description:o.z.string().max(2e3).optional().describe("Description"),echo:o.z.boolean().optional().describe("false → lean response (default true)"),variables:o.z.array(o.z.object({name:o.z.string().min(1).max(64).describe("Variable name"),value:o.z.string().min(1).max(500).describe("Initial value"),unit:o.z.string().max(32).optional().describe("Unit abbreviation"),description:o.z.string().max(2e3).optional().describe("Description")})).optional().describe("Array form: batch variable creation. Atomic — all or none."),idempotency_key:o.z.string().max(128).optional().describe("Dedup key for retries")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_create_variable",async e=>{const{createVariableHandler:t}=await Promise.resolve().then(()=>(bn(),mn));return t(e)})),Ua("atoms_delete_variable",{title:"Delete Project Variable",description:"Delete a project variable. Refuses by default if any items reference it.\n\nArgs:\n - project_id (string, UUID): Project containing the variable\n - name (string): Variable name to delete\n - force (bool, optional): Delete even if items still reference it (default false)\n\nReturns:\n { deleted, name, referenced_by_items, warning? }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).describe("Variable name to delete"),force:o.z.boolean().optional().describe("Delete even if items reference it (default false)"),confirmation_token:o.z.string().max(500).optional().describe("Token from a prior preview call (only used when ATOMS_MCP_REQUIRE_CONFIRMATION is set)")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_delete_variable",async e=>{const{deleteVariableHandler:t}=await Promise.resolve().then(()=>(bn(),mn));return t(e)})),Ua("atoms_list_domains",{title:"List Project Domains",description:"List all domain tags registered in a project's taxonomy, with item counts.\n\nArgs:\n - project_id (string, UUID): Project to inspect\n\nReturns:\n { domains: [{ name, item_count }], total }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_list_domains",async e=>{const{listDomainsHandler:t}=await Promise.resolve().then(()=>(An(),vn));return t(e)})),Ua("atoms_create_domain",{title:"Create Project Domain",description:'Register a new domain tag in the project taxonomy.\n\nOnce created, items can be tagged with this domain via atoms_create_item or atoms_update_item.\n\nArgs:\n - project_id (string, UUID): Project to add the domain to\n - name (string): Domain name (lowercased automatically, e.g., "safety", "can-bus")\n\nReturns:\n { domain: { name }, message }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).describe("Domain name")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_create_domain",async e=>{const{createDomainHandler:t}=await Promise.resolve().then(()=>(An(),vn));return t(e)})),Ua("atoms_list_levels",{title:"List Project Levels",description:"List the project's level taxonomy in order, with each level's L# (positional index) and item count.\n\nArgs:\n - project_id (string, UUID): Project to list levels for\n\nReturns:\n { levels: [{ name, prefix, item_count }], total }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_list_levels",async e=>{const{listLevelsHandler:t}=await Promise.resolve().then(()=>(Gr(),$r));return t(e)})),Ua("atoms_create_level",{title:"Create Project Level",description:'Register a new level in the project taxonomy so items can be tagged with it and it shows in the Strata view. Appended to the ordered level list; its L# is the next index. Names are user-defined labels (lowercased automatically); matching is case-insensitive.\n\nArgs:\n - project_id (string, UUID): Project to add the level to\n - name (string): Level name, e.g. "feature", "system", "subsystem"\n\nReturns:\n { level: { name, prefix }, message }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).describe("Level name (user-defined label)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_create_level",async e=>{const{createLevelHandler:t}=await Promise.resolve().then(()=>(Gr(),$r));return t(e)})),Ua("atoms_list_fields",{title:"List Project Fields",description:'List the project\'s custom field definitions (project-scoped key-value slots on items, e.g. "Verification Method"), with counts of items carrying a value.\n\nField values are set per item via atoms_create_item / atoms_update_item fields.\n\nArgs:\n - project_id (string, UUID): Project to inspect\n\nReturns:\n { fields: [{ name, type, options, item_count }], total }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_list_fields",async e=>{const{listFieldsHandler:t}=await Promise.resolve().then(()=>(ui(),Kr));return t(e)})),Ua("atoms_create_field",{title:"Create Project Field",description:'Define a project custom field so items can carry a value for it (shown as a Matrix column, e.g. "Verification Method").\n\nThe name keeps its casing; uniqueness is case-insensitive. Type is one of text, long, bool, date, person, select, number, link. Select fields require options. Field definitions never carry visibility rules, permissions, or workflow logic.\n\nArgs:\n - project_id (string, UUID): Project to define the field in\n - name (string): Field name, 1-60 characters (e.g. "Verification Method", "Essential Output?")\n - type (string, optional): Defaults to text\n - options (string[], optional): Required when type=select\n - scope (string, optional): project (default) or organization (org admin only)\n\nReturns:\n { field: { name, type, options }, message }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(60).describe("Field name (display name, 1-60 chars)"),type:o.z.enum(["text","long","bool","date","person","select","number","link"]).optional().describe("Field type, defaults to text"),options:o.z.array(o.z.string().min(1).max(120)).max(100).optional().describe("Allowed values for select fields"),scope:o.z.enum(["project","organization"]).optional().describe("Create in this project or copy to every project in the organization")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_create_field",async e=>{const{createFieldHandler:t}=await Promise.resolve().then(()=>(ui(),Kr));return t(e)})),Ua("atoms_delete_field",{title:"Delete Project Field",description:"Delete a project field definition. Existing item values are left in item JSON but no longer render as Matrix columns until a matching field is created again.\n\nArgs:\n - project_id (string, UUID): Project containing the field\n - name (string): Field name to delete",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(60).describe("Field name")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_delete_field",async e=>{const{deleteFieldHandler:t}=await Promise.resolve().then(()=>(ui(),Kr));return t(e)})),Ua("atoms_reorder_fields",{title:"Reorder Project Fields",description:"Reorder project field definitions. Definition order drives the Column Picker listing and a fresh user's Matrix column order.\n\nOrdering only: no definition is added, dropped, renamed, or retyped, and no item value moves. Use this instead of deleting and recreating definitions to change their order.\n\nArgs:\n - project_id (string, UUID): Project containing the fields\n - names (string[]): Every existing field name exactly once, in the order you want them. A list that is not a permutation of the current names is refused, not partially applied.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),names:o.z.array(o.z.string().min(1).max(60)).describe("Every existing field name exactly once, in the desired order")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_reorder_fields",async e=>{const{reorderFieldsHandler:t}=await Promise.resolve().then(()=>(ui(),Kr));return t(e)})),Ua("atoms_update_domain",{title:"Rename Project Domain",description:"Rename a domain tag. Updates the taxonomy and propagates to all tagged items.\n\nUse dry_run=true first to see how many items will be affected before committing.\n\nArgs:\n - project_id (string, UUID): Project containing the domain\n - name (string): Current domain name\n - new_name (string): New domain name\n - dry_run (bool, optional): If true, return impact count without making changes (default false)\n\nReturns (dry_run=false):\n { domain: { name }, renamed_from, items_updated, message }\n\nReturns (dry_run=true):\n { dry_run: true, rename: { from, to }, items_affected, message }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).describe("Current domain name"),new_name:o.z.string().min(1).max(64).describe("New domain name"),dry_run:o.z.boolean().optional().describe("Preview impact without applying (default false)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_update_domain",async e=>{const{updateDomainHandler:t}=await Promise.resolve().then(()=>(An(),vn));return t(e)})),Ua("atoms_delete_domain",{title:"Delete Project Domain",description:"Delete a domain tag from the project taxonomy.\n\nRefuses by default if any items are tagged with it. With force=true, deletes the\ndomain and strips the tag from all items.\n\nArgs:\n - project_id (string, UUID): Project containing the domain\n - name (string): Domain name to delete\n - force (bool, optional): Strip from items and delete anyway (default false)\n\nReturns:\n { deleted, name, items_updated, message }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).describe("Domain name to delete"),force:o.z.boolean().optional().describe("Strip from all items and delete (default false)"),confirmation_token:o.z.string().max(500).optional().describe("Token from a prior preview call (only used when ATOMS_MCP_REQUIRE_CONFIRMATION is set)")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_delete_domain",async e=>{const{deleteDomainHandler:t}=await Promise.resolve().then(()=>(An(),vn));return t(e)})),La({appName:"summary",htmlFile:"summary-app.html",toolName:"atoms_project_summary",title:"Project Compliance Summary",description:'One-call project health and compliance dashboard.\n\nReturns item counts by type, test execution status, requirement coverage\n(overall and by domain), and recent change activity.\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive dashboard with charts.\nFalls back to JSON for non-UI clients.\n\nArgs:\n - project_id (string, UUID): Project to summarize\n\nReturns:\n { project_name, counts, test_status, coverage, coverage_by_domain, recent_changes, last_updated }\n\nExamples:\n - "Give me a compliance snapshot" → atoms_project_summary(project_id)\n - "How\'s our test coverage?" → atoms_project_summary(project_id)',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Fa("atoms_project_summary",async e=>{const{projectSummaryHandler:t}=await Promise.resolve().then(()=>(zn(),Rn));return t(e)})}),La({appName:"browse",htmlFile:"browse-app.html",toolName:"atoms_browse",title:"Browse ATOMS Items",description:'View and filter items in an ATOMS project with a visual browser.\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive filterable list\nwith expandable item details. Falls back to JSON for non-UI clients.\n\nArgs:\n - project_id (string, UUID): The project to browse\n - type (string, optional): Filter by type (requirement, test-case, note, table)\n - domain (string, optional): Filter by domain tag\n - level (string, optional): Filter by level (System, Subsystem, Component)\n - query (string, optional): Full-text search query\n - limit (number, optional): Max results (default 25, max 100)\n - offset (number, optional): Pagination offset (default 0)\n\nReturns:\n { items: [...], filters: { domains, levels, types }, meta: { total_count, limit, offset, has_more } }\n\nExamples:\n - "Show me the requirements" → atoms_browse(project_id, type="requirement")\n - "Browse safety items" → atoms_browse(project_id, domain="Safety")\n - "Find braking requirements" → atoms_browse(project_id, query="braking")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),type:o.z.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),domain:o.z.string().max(64).optional().describe("Filter by domain tag"),level:o.z.string().max(32).optional().describe("Filter by level (System, Subsystem, Component)"),query:o.z.string().max(1e3).optional().describe("Full-text search query"),limit:o.z.number().int().min(1).max(100).default(25).describe("Max results (default 25, max 100)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset (default 0)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Fa("atoms_browse",async e=>{const{browseHandler:t}=await Promise.resolve().then(()=>(Pn(),Hn));return t(e)})}),Ua("atoms_impact_analysis",{title:"Analyze Impact of Changing an Item",description:'Analyze the blast radius of changing a specific item.\n\nTraverses the relationship graph from the given item and returns every item that\nwould be affected by a change — with their types, depths, and full relationship paths.\n\nArgs:\n - project_id (string, UUID): Project containing the item\n - item_id (string): Item to analyze (e.g., "REQ-001")\n - direction (string, optional): "downstream" (default) | "upstream" | "both"\n - downstream: what this item affects (children, verified_by)\n - upstream: what affects this item (parents, verifies)\n - both: full bidirectional traversal\n - depth (integer, optional): Max traversal depth. Omit for full depth (all reachable nodes).\n - include_variable_refs (boolean, optional): Reserved for future variable-aware impact. Default true.\n\nReturns:\n { root: { item_id, title, type }, impacted_items: [{ item_id, title, type, depth, relationship_path }], summary: { total_impacted, by_type, max_depth_reached } }\n\nExamples:\n - "What breaks if I change REQ-001?" → atoms_impact_analysis(project_id, "REQ-001")\n - "What\'s upstream of TC-005?" → atoms_impact_analysis(project_id, "TC-005", direction="upstream")\n - "Show direct dependencies only" → atoms_impact_analysis(project_id, "REQ-001", depth=1)\n\nErrors:\n - "Item not found" → verify item_id exists in the project',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID to analyze (e.g., REQ-001)"),direction:o.z.enum(["downstream","upstream","both"]).default("downstream").describe("Traversal direction (default: downstream)"),depth:o.z.number().int().min(1).optional().describe("Max traversal depth. Omit for full depth."),include_variable_refs:o.z.boolean().default(!0).describe("Reserved for variable-aware impact (future). Default true.")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_impact_analysis",async e=>{const{impactAnalysisHandler:t}=await Promise.resolve().then(()=>(Ln(),$n));return t(e)})),Ua("atoms_list_baselines",{title:"List ATOMS Baselines",description:"List named baselines (named project snapshots) for a project, newest first.\n\nA baseline is a labeled moment in time. Use atoms_create_baseline to make one,\natoms_diff_baselines to compare two, and atoms_restore_baseline to roll back.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),limit:o.z.number().int().min(1).max(100).default(50).describe("Max results (default 50, max 100)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_list_baselines",async e=>{const{listBaselinesHandler:t}=await Promise.resolve().then(()=>(la(),Wn));return t(e)})),Ua("atoms_create_baseline",{title:"Create ATOMS Baseline",description:"Create a named baseline (snapshot label) at the current moment for a project.\n\nThe baseline records a name + timestamp. It does NOT copy item data; the project\nstate at that moment is reconstructed via temporal queries against item_revisions.\nNames must be unique per project (case-insensitive).",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(200).describe("Baseline name (1-200 chars, unique per project)"),description:o.z.string().max(2e3).optional().describe("Optional description (max 2000 chars)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_create_baseline",async e=>{const{createBaselineHandler:t}=await Promise.resolve().then(()=>(la(),Wn));return t(e)})),Ua("atoms_lock_baseline",{title:"Lock ATOMS Baseline",description:"Lock a baseline so it becomes audit-grade immutable. Admin only. One-way: there is no unlock.\n\nAfter locking, the baseline's name, description, and snapshot_at cannot be changed,\nand it cannot be deleted. Use for regulatory submissions and DRBs.",inputSchema:{baseline_id:o.z.string().uuid().describe("UUID of the baseline to lock")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_lock_baseline",async e=>{const{lockBaselineHandler:t}=await Promise.resolve().then(()=>(la(),Wn));return t(e)})),Ua("atoms_diff_baselines",{title:"Diff ATOMS Baselines",description:"Compute the diff between two baselines: which items were added, removed, or modified.\n\nReturns a summary plus a paginated items array. Pass detail=true to include\nper-item field-level diffs (slower for large projects).",inputSchema:{baseline_a_id:o.z.string().uuid().describe("UUID of the first (older) baseline"),baseline_b_id:o.z.string().uuid().describe("UUID of the second (newer) baseline"),detail:o.z.boolean().default(!1).describe("Include per-item field-level diffs (default false)"),limit:o.z.number().int().min(1).max(200).default(50).describe("Max items per page (default 50)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_diff_baselines",async e=>{const{diffBaselinesHandler:t}=await Promise.resolve().then(()=>(la(),Wn));return t(e)})),Ua("atoms_restore_baseline",{title:"Restore from ATOMS Baseline",description:"Restore project state to a baseline. Admin only. Preview-by-default.\n\nCall with confirm=false (default) for a dry run that returns items_to_restore count.\nCall with confirm=true to execute: each item present at the baseline gets a new\nrevision matching its historical state, event_source='restore'. Items added AFTER\nthe baseline are NOT deleted. Always recoverable via further history.",inputSchema:{baseline_id:o.z.string().uuid().describe("UUID of the baseline to restore from"),confirm:o.z.boolean().default(!1).describe("Set true to execute; false (default) returns a preview")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_restore_baseline",async e=>{const{restoreBaselineHandler:t}=await Promise.resolve().then(()=>(la(),Wn));return t(e)})),Ua("atoms_create_analysis",{title:"Create HARA / DFMEA Analysis",description:'Create a new safety analysis (HARA or DFMEA) with one empty row per source requirement.\n\nRequires editor or admin role. Structure matches analyses created in the ATOMS web app.\n\nArgs:\n - project_id (string, UUID): Target project\n - subtype (string): hara | dfmea\n - title (string, optional): Analysis title (default "New HARA" / "New DFMEA")\n - source_req_ids (string[], optional, max 50): Requirement IDs to seed rows from.\n Each must exist, be a plain requirement, and not itself be an analysis row.\n - revision (string, optional): Revision label (default "1.0")\n\nReturns:\n { id (e.g. "HARA-001" / "DFMEA-001"), subtype, title, revision, rows: [{ id, source_req }],\n link_warnings?: [{ row_id, source_req, message }], warning? }\n rows lists every created row. If any row could not be attached to the analysis, it is\n named in link_warnings and warning explains the repair (atoms_link_items with type\n \'parent\', from_id=<row id>, to_id=<analysis id>); such rows will not appear in\n atoms_get_analysis until relinked.\n\nSide effects:\n - Creates the analysis parent item plus one row item (SG-nnn / FM-nnn) per source requirement\n - Links each row to the parent (dual-written to the relationship shadow table)\n - Logs each created item to change_history with actor=\'mcp_<client>\'',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the target project"),subtype:o.z.enum(["hara","dfmea"]).describe("Analysis subtype"),title:o.z.string().min(1).max(500).optional().describe("Analysis title"),source_req_ids:o.z.array(o.z.string().min(1).max(20)).max(50).optional().describe("Requirement IDs to seed rows from (0-50)"),revision:o.z.string().min(1).max(32).optional().describe("Revision label (default 1.0)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Fa("atoms_create_analysis",async e=>{const{createAnalysisHandler:t}=await Promise.resolve().then(()=>($a(),wa));return t(e)})),Ua("atoms_fill_row",{title:"Fill Analysis Row Fields",description:"Fill fields on one HARA / DFMEA analysis row (SG-nnn / FM-nnn).\n\nRequires editor or admin role. Written fields are marked as MCP-sourced so the\nweb app shows their provenance. The computed level (ASIL / RPN) is derived and\nnever stored.\n\nArgs:\n - project_id (string, UUID): Project containing the row\n - row_id (string): Analysis row ID (e.g. \"SG-001\", \"FM-003\")\n - fields (object): Field name to value map. Allowed keys:\n hara: failure_mode, operating_scenario, severity (S0-S3), exposure (E0-E4),\n controllability (C0-C3), safe_state, ftti, rationale, effect, title\n dfmea: failure_mode, cause, severity (1-10), occurrence (1-10), detection (1-10),\n rationale, effect\n 'effect' writes the row's long text body. dfmea failure_mode also becomes the row title.\n dfmea ratings accept numbers and are stored as strings.\n\nReturns:\n { row_id, subtype, written_fields, computed_level, asil_propagated_to? }\n\nSide effects:\n - Saves the row with stale-write protection and logs to change_history\n - hara only: if the row is linked and its computed ASIL changed, updates each\n linked requirement's asil / asil_source (each update is history-logged)",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),row_id:o.z.string().min(1).max(20).describe("Analysis row ID (e.g. SG-001, FM-003)"),fields:o.z.record(o.z.string().max(64),o.z.union([o.z.string().max(5e4),o.z.number()])).describe("Field name to value map (see description for allowed keys per subtype)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_fill_row",async e=>{const{fillRowHandler:t}=await Promise.resolve().then(()=>($a(),wa));return t(e)})),Ua("atoms_get_analysis",{title:"Get HARA / DFMEA Analysis",description:'Get a full analysis view: every row with its computed level (ASIL / RPN) and\ngap / critical / stale classifications, plus summary counts.\n\nClassifications match the ATOMS web app exactly (same rules, same thresholds).\n\nArgs:\n - project_id (string, UUID): Project containing the analysis\n - analysis_id (string): Analysis ID (e.g. "HARA-001", "DFMEA-002")\n\nReturns:\n { analysis: { id, title, subtype, scheme, revision },\n rows: [{ id, title, source_req, effect, <subtype fields>, computed_level, is_gap, gap_rule,\n is_critical, is_stale, mitigated_by, link_roles, approved, approved_at, mcp_fields }],\n counts: { rows, gaps, critical, stale, approved, linked } }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),analysis_id:o.z.string().min(1).max(20).describe("Analysis ID (e.g. HARA-001, DFMEA-002)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_get_analysis",async e=>{const{getAnalysisHandler:t}=await Promise.resolve().then(()=>($a(),wa));return t(e)})),Ua("atoms_link_mitigation",{title:"Link Analysis Row to Mitigating Requirement",description:'Link a HARA / DFMEA row to the technical requirement that mitigates it.\n\nRequires editor or admin role.\n\nArgs:\n - project_id (string, UUID): Project containing both items\n - row_id (string): Analysis row ID (e.g. "SG-001", "FM-003")\n - req_id (string): Target requirement ID (must be a plain requirement, not an analysis row)\n - role (string, dfmea only, REQUIRED for dfmea): prevention | detection | mitigation.\n Must be omitted for hara rows.\n - override (boolean, optional, default false): hara only. When the target already\n carries a different asil, the call fails with a structured error\n (details.code=\'asil_conflict\') unless override=true; the override is\n history-logged like a dialog accept.\n\nReturns:\n { row_id, req_id, type: "mitigated_by", role, asil_written? }\n\nSide effects:\n - Adds the mitigated_by/mitigates relationship (JSONB + shadow table, one transaction)\n - hara only: writes the row\'s computed ASIL onto the target requirement\n (data.asil + data.asil_source) with a history entry recording previous/new values\n - dfmea: never modifies any field on the target requirement',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),row_id:o.z.string().min(1).max(20).describe("Analysis row ID (e.g. SG-001, FM-003)"),req_id:o.z.string().min(1).max(20).describe("Target requirement ID (e.g. REQ-042)"),role:o.z.enum(["prevention","detection","mitigation"]).optional().describe("Mitigation role. Required for dfmea rows; must be omitted for hara rows."),override:o.z.boolean().optional().describe("hara only: apply the row's ASIL over a conflicting existing value (history-logged)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_link_mitigation",async e=>{const{linkMitigationHandler:t}=await Promise.resolve().then(()=>($a(),wa));return t(e)})),Ua("atoms_get_gaps",{title:"Get Analysis Gap Rows",description:'List only the gap rows of a HARA / DFMEA analysis, each naming the rule that matched.\n\nGap rules (identical to the web app):\n hara: unmitigated row with ASIL A-D ("asil <X> unmitigated")\n dfmea: unmitigated row with RPN >= 100 ("rpn >= 100") or severity >= 9 ("severity >= 9")\n\nArgs:\n - project_id (string, UUID): Project containing the analysis\n - analysis_id (string): Analysis ID (e.g. "HARA-001", "DFMEA-002")\n\nReturns:\n { analysis_id, subtype, gaps: [{ id, title, source_req, computed_level, rule }], count }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),analysis_id:o.z.string().min(1).max(20).describe("Analysis ID (e.g. HARA-001, DFMEA-002)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Fa("atoms_get_gaps",async e=>{const{getGapsHandler:t}=await Promise.resolve().then(()=>($a(),wa));return t(e)}))}});B(),$(),Ne(),M();var Qa=l.createRequire("undefined"==typeof document?require("url").pathToFileURL(__filename).href:p&&"SCRIPT"===p.tagName.toUpperCase()&&p.src||new URL("index.cjs",document.baseURI).href)("../package.json"),Ga=process.argv.slice(2)[0];(async function(){switch(Ga){case"login":{const{login:e}=await Promise.resolve().then(()=>(Ye(),Le));try{const{email:t}=await e();process.stderr.write(`\n ✓ Authenticated as ${t}\n`),process.stderr.write(" ✓ Credentials saved to ~/.atoms/credentials.json\n\n"),process.stderr.write(" Next steps:\n"),process.stderr.write(" $ claude mcp add atoms -- npx -y @atoms-tech/atoms-mcp\n"),process.stderr.write("\n Or add to Claude Desktop (Settings → MCP → Edit Config):\n"),process.stderr.write(' {\n "mcpServers": {\n "atoms": {\n "command": "npx",\n "args": ["-y", "@atoms-tech/atoms-mcp"]\n }\n }\n }\n\n')}catch(e){process.stderr.write(`\n ✗ ${e instanceof Error?e.message:String(e)}\n\n`),process.exit(1)}break}case"whoami":{const{getValidToken:e}=await Promise.resolve().then(()=>(Re(),be));try{const{email:t,user_id:r}=await e();process.stderr.write(`\n ✓ Logged in as ${t}\n User ID: ${r}\n\n`)}catch(e){process.stderr.write(`\n ✗ Not authenticated: ${e instanceof Error?e.message:String(e)}\n Run: npx @atoms-tech/atoms-mcp login\n\n`),process.exit(1)}break}case"logout":{const{clearCredentials:e}=await Promise.resolve().then(()=>(oe(),J));await e(),process.stderr.write("Logged out. Credentials removed.\n"),process.stderr.write("Run 'npx @atoms-tech/atoms-mcp login' to authenticate again.\n");break}case"--version":case"-v":process.stderr.write(`@atoms-tech/atoms-mcp v${Qa.version}\n`);break;case"--help":case"-h":process.stderr.write("ATOMS MCP Server — AI agent integration for requirements management\n\nUsage:\n npx @atoms-tech/atoms-mcp Start MCP server (stdio)\n npx @atoms-tech/atoms-mcp login Authenticate with ATOMS.tech\n npx @atoms-tech/atoms-mcp logout Switch account / clear credentials\n npx @atoms-tech/atoms-mcp whoami Show current user\n npx @atoms-tech/atoms-mcp --version Show version\n");break;default:{process.stderr.write("[atoms-mcp] Starting MCP server via stdio...\n");{const{getValidToken:e,readValidToken:t}=await Promise.resolve().then(()=>(Re(),be)),{runExclusiveAuth:r}=await Promise.resolve().then(()=>(he(),de)),{login:i}=await Promise.resolve().then(()=>(Ye(),Le));try{let n;try{n=(await e()).email}catch(e){process.stderr.write(`[atoms-mcp] Could not use the saved session: ${e instanceof Error?e.message:String(e)}\n`),process.stderr.write("[atoms-mcp] Starting login flow...\n");const a=async()=>{const e=await t();if(!e)throw new Error("no valid token yet");return{email:e.email}};n=(await r(a,async()=>({email:(await i()).email}))).email}process.stderr.write(`[atoms-mcp] Authenticated as ${n}\n`)}catch(e){process.stderr.write(`[atoms-mcp] Login failed: ${e instanceof Error?e.message:String(e)}\n[atoms-mcp] Starting server without auth. Tools will fail until you run: npx @atoms-tech/atoms-mcp login\n`)}}try{const t=await De(),r=Ce(),i=await async function(e,t){const r=process.env.ATOMS_MCP_ORG_ID?.trim();if(r)return r;const{data:i,error:n}=await e.from("org_members").select("org_id, joined_at").eq("user_id",t).order("joined_at",{ascending:!0}).limit(1).maybeSingle();return n?(process.stderr.write(`[atoms-mcp] Could not resolve session org: ${n.message}\n`),null):i?.org_id??null}(t,r),n=await async function(e,t,r){if(!r)return{role:null,is_member:!1,effective:H};const{data:i,error:n}=await e.rpc("mcp_resolve_policy",{p_user_id:t,p_org_id:r});return n?(process.stderr.write(`[atoms-mcp] mcp_resolve_policy failed (${n.code}): ${n.message}. Falling back to fail-closed policy.\n`),{role:null,is_member:!1,effective:U}):function(e){if(!e||"object"!=typeof e)return{role:null,is_member:!1,effective:H};const t=e,r="string"==typeof t.role?t.role:null,i=!0===t.is_member,n=t.effective??{},a=(e,t)=>Array.isArray(e)?e.filter(e=>"string"==typeof e):t,s=(e,t)=>"boolean"==typeof e?e:t,o=n.project_scope,d=Array.isArray(o)&&o.length>0?o.filter(e=>"string"==typeof e):null;return{role:r,is_member:i,effective:{read_only:s(n.read_only,H.read_only),lockdown:s(n.lockdown,H.lockdown),block_destructive:s(n.block_destructive,H.block_destructive),block_bulk_import:s(n.block_bulk_import,H.block_bulk_import),cross_project_browse:s(n.cross_project_browse,H.cross_project_browse),allowed_toolsets:a(n.allowed_toolsets,H.allowed_toolsets),forbidden_tools:a(n.forbidden_tools,H.forbidden_tools),project_scope:d,require_confirmation_for:a(n.require_confirmation_for,H.require_confirmation_for)}}}(i)}(t,r,i);e={effective:n.effective,role:n.role,org_id:i},C=e.effective,q=e.org_id,n.is_member&&i?process.stderr.write(`[atoms-mcp] Org policy loaded: org=${i.slice(0,8)}… role=${n.role??"?"} read_only=${n.effective.read_only} lockdown=${n.effective.lockdown}\n`):process.stderr.write("[atoms-mcp] No org membership detected — running with permissive default policy.\n")}catch(e){process.stderr.write(`[atoms-mcp] Could not resolve session policy (${e instanceof Error?e.message:String(e)}). Running with permissive default — RLS still enforces row-level access.\n`)}process.stderr.write(`[atoms-mcp] Tool registry: ${function(){const e=L(),t=N(),r=[];r.push(e?"read-only":"read+write"),null===t?r.push("all toolsets"):(r.push(`toolsets=${[...t.allowed].sort().join(",")||"(none — only always-on tools)"}`),t.unknown.length>0&&r.push(`unknown=${t.unknown.join(",")}`));const i=process.env.ATOMS_MCP_PROJECT_ID?.trim();return i&&r.push(`project_scope=${i.slice(0,8)}…`),("1"===process.env.ATOMS_MCP_LOCKDOWN||"true"===process.env.ATOMS_MCP_LOCKDOWN)&&r.push("lockdown=on"),r.join(" | ")}()}\n`);const{server:t}=await Promise.resolve().then(()=>(Ja(),Na)),r=new m.StdioServerTransport;await t.connect(r),process.stderr.write("[atoms-mcp] MCP server running. Waiting for tool calls...\n")}}var e})().catch(e=>{process.stderr.write(`[atoms-mcp] Fatal: ${e instanceof Error?e.message:String(e)}\n`),process.exit(1)});
2
+ "use strict";var e=require("fs/promises"),t=require("os"),r=require("path"),i=require("@supabase/supabase-js"),n=require("http"),a=require("crypto"),s=require("url"),o=require("zod"),d=require("@modelcontextprotocol/ext-apps/server"),c=require("@modelcontextprotocol/sdk/server/mcp.js"),l=require("module"),m=require("@modelcontextprotocol/sdk/server/stdio.js"),p="undefined"!=typeof document?document.currentScript:null;function u(e){return e&&e.__esModule?e:{default:e}}var _,f,h,g,y,w,b,v=u(e),j=u(r),S=u(a),x=Object.defineProperty,k=Object.getOwnPropertyNames,E=(e,t,r)=>function(){if(r)throw r[0];try{return e&&(t=(0,e[k(e)[0]])(e=0)),t}catch(e){throw r=[e],e}},I=(e,t)=>{for(var r in t)x(e,r,{get:t[r],enumerable:!0})};function A(e){return b.get(e)}var R=E({"src/core/tool-catalog.ts"(){_=new Set(["atoms_status","atoms_list_projects"]),f=new Set(["atoms_create_item","atoms_update_item","atoms_delete_item","atoms_restore_item","atoms_link_items","atoms_bulk_import","atoms_record_test_result","atoms_record_test_results","atoms_create_variable","atoms_update_variable","atoms_delete_variable","atoms_create_domain","atoms_update_domain","atoms_delete_domain","atoms_create_level","atoms_create_field","atoms_delete_field","atoms_reorder_fields","atoms_create_baseline","atoms_lock_baseline","atoms_restore_baseline","atoms_create_analysis","atoms_fill_row","atoms_link_mitigation"]),h=new Set(["atoms_delete_item","atoms_delete_variable","atoms_delete_domain","atoms_delete_field","atoms_restore_baseline"]),g=new Set(["atoms_bulk_import"]),y={items:["atoms_list_items","atoms_get_item","atoms_search","atoms_semantic_search","atoms_browse","atoms_get_history","atoms_create_item","atoms_update_item","atoms_delete_item","atoms_restore_item","atoms_bulk_import"],traceability:["atoms_trace","atoms_link_items","atoms_export_mermaid","atoms_impact_analysis"],coverage:["atoms_get_coverage","atoms_verification_status","atoms_record_test_result","atoms_record_test_results","atoms_project_summary","atoms_list_assets"],variables:["atoms_list_variables","atoms_get_variable","atoms_create_variable","atoms_update_variable","atoms_delete_variable"],domains:["atoms_list_domains","atoms_create_domain","atoms_update_domain","atoms_delete_domain","atoms_list_levels","atoms_create_level","atoms_list_fields","atoms_create_field","atoms_delete_field","atoms_reorder_fields"],baselines:["atoms_list_baselines","atoms_create_baseline","atoms_lock_baseline","atoms_diff_baselines","atoms_restore_baseline"],analysis:["atoms_create_analysis","atoms_fill_row","atoms_get_analysis","atoms_link_mitigation","atoms_get_gaps"]},w=Object.keys(y),b=new Map;for(const[e,t]of Object.entries(y))for(const r of t)b.set(r,e)}});function O(e,t){if(_.has(t))return{allowed:!0};if(e.lockdown&&!new Set(["atoms_list_items","atoms_get_item","atoms_search","atoms_browse"]).has(t))return{allowed:!1,reason:"lockdown"};if(e.forbidden_tools.includes(t))return{allowed:!1,reason:"forbidden_tool"};if(e.read_only&&f.has(t))return{allowed:!1,reason:"read_only"};if(e.block_destructive&&h.has(t))return{allowed:!1,reason:"block_destructive"};if(e.block_bulk_import&&g.has(t))return{allowed:!1,reason:"block_bulk_import"};const r=A(t);return void 0===r||e.allowed_toolsets.includes(r)?{allowed:!0}:{allowed:!1,reason:"toolset_disabled"}}function z(e,t){return O(e,t).allowed}function D(e){switch(e){case"lockdown":return"MCP is in lockdown mode for your role — only read-only browse is available.";case"read_only":return"Your org policy puts MCP in read-only mode. Mutating tools are not exposed.";case"block_destructive":return"Your org policy blocks destructive operations (delete tools).";case"block_bulk_import":return"Your org policy blocks bulk import.";case"forbidden_tool":return"This tool is on your org's forbidden list.";case"toolset_disabled":return"This tool's toolset is not enabled in your org policy."}}var H,U,C,q,T=E({"src/core/policy.ts"(){R()}}),M=E({"src/core/types.ts"(){H={read_only:!1,lockdown:!1,block_destructive:!1,block_bulk_import:!1,cross_project_browse:!0,allowed_toolsets:["items","traceability","coverage","variables","domains","baselines"],forbidden_tools:[],project_scope:null,require_confirmation_for:[]},U={read_only:!0,lockdown:!0,block_destructive:!0,block_bulk_import:!0,cross_project_browse:!1,allowed_toolsets:[],forbidden_tools:[],project_scope:[],require_confirmation_for:[]}}});function P(){return C}var $=E({"src/middleware/session-policy.ts"(){M(),C=H,q=null}});function N(){const e=process.env.ATOMS_MCP_TOOLSETS?.trim();if(!e)return null;const t=e.split(",").map(e=>e.trim()).filter(Boolean);if(0===t.length)return null;const r=new Set,i=[];for(const e of t)w.includes(e)?r.add(e):i.push(e);return{allowed:r,unknown:i}}function L(){const e=process.env.ATOMS_MCP_READ_ONLY;return"1"===e||"true"===e?.toLowerCase()}function F(e){if(L()&&f.has(e))return!1;if(_.has(e))return!0;const t=N();if(null===t)return z(P(),e);const r=A(e);return!!r&&!!t.allowed.has(r)&&z(P(),e)}var W,V,B=E({"src/middleware/tool-registry.ts"(){R(),T(),$()}}),J={};async function Q(){try{const t=await e.readFile(V,"utf-8"),r=JSON.parse(t);return r.access_token&&r.refresh_token?r:null}catch{return null}}async function G(t){await e.mkdir(W,{recursive:!0,mode:448}),await e.writeFile(V,JSON.stringify(t,null,2),{mode:384})}async function Y(){const e=await Q();return!!e&&e.expires_at>Date.now()+6e4}function K(e){return e.expires_at>Date.now()+6e4}async function Z(){try{await e.unlink(V)}catch{}}function X(){return V}I(J,{clearCredentials:()=>Z,getCredentialsPath:()=>X,hasValidCredentials:()=>Y,isTokenValid:()=>K,readCredentials:()=>Q,writeCredentials:()=>G});var ee,te,re,ie,ne,ae,se,oe=E({"src/auth/token-store.ts"(){W=r.join(t.homedir(),".atoms"),V=r.join(W,"credentials.json")}}),de={};async function ce(){try{await e.mkdir(ee,{recursive:!0,mode:448});const t=await e.open(te,"wx");try{await t.writeFile(`${process.pid} ${Date.now()}`)}finally{await t.close()}return!0}catch(e){if("EEXIST"===e.code)return!1;throw e}}async function le(){try{await e.unlink(te)}catch{}}async function me(){try{const t=await e.stat(te);return Date.now()-t.mtimeMs>re}catch{return!1}}async function pe(e,t,r=se){const i=r.now()+ie;for(;;){if(await r.tryAcquire())try{try{return await e()}catch{}return await t()}finally{await r.release()}try{return await e()}catch{}if(await r.isStale())await r.release();else{if(r.now()>i)return await t();await r.wait(ne)}}}I(de,{runExclusiveAuth:()=>pe});var ue,_e,fe,he=E({"src/auth/lock.ts"(){ee=r.join(t.homedir(),".atoms"),te=r.join(ee,".auth.lock"),re=7e4,ie=12e4,ne=300,ae=e=>new Promise(t=>setTimeout(t,e)),se={now:Date.now,wait:ae,tryAcquire:ce,release:le,isStale:me}}}),ge={};function ye(e){return e.trim().replace(/\/+$/,"")}I(ge,{ATOMS_APP_URL:()=>fe,ATOMS_SUPABASE_ANON_KEY:()=>_e,ATOMS_SUPABASE_URL:()=>ue,resolveUrl:()=>ye});var we=E({"src/config.ts"(){ue=ye(process.env.ATOMS_SUPABASE_URL??"https://gmebjyhomsbvhrxffzre.supabase.co"),_e=process.env.ATOMS_SUPABASE_ANON_KEY??"sb_publishable_b49MUAB8XCrQiF7x5b9lUA_w1aplSBH",fe=process.env.ATOMS_APP_URL??"https://atoms.tech"}}),be={};async function ve(){const e=process.env.ATOMS_ACCESS_TOKEN;if(e){const t=Se(e);return{access_token:e,refresh_token:"",user_id:t.sub,email:t.email??""}}const t=await Q();if(t&&t.expires_at>Date.now()+6e4){const e=Se(t.access_token);return{access_token:t.access_token,refresh_token:t.refresh_token,user_id:e.sub,email:e.email??t.user_email??""}}return null}async function je(){const e=await ve();if(e)return e;const t=await Q();if(!t)throw new Error("Not authenticated. Run 'npx @atoms-tech/atoms-mcp login' to connect your ATOMS account.");return pe(async()=>{const e=await ve();if(e)return e;throw new Error("no fresh token yet")},()=>async function(e){process.stderr.write("[atoms-mcp] Refreshing access token...\n");const t=i.createClient(ue,_e);let r=await t.auth.refreshSession({refresh_token:e.refresh_token});if(r.error||!r.data.session){const i=await Q();if(i&&i.expires_at>Date.now()+6e4){const e=Se(i.access_token);return{access_token:i.access_token,refresh_token:i.refresh_token,user_id:e.sub,email:e.email??i.user_email??""}}i&&i.refresh_token&&i.refresh_token!==e.refresh_token&&(process.stderr.write("[atoms-mcp] Refresh token was rotated by another session; retrying with the latest...\n"),r=await t.auth.refreshSession({refresh_token:i.refresh_token}))}if(r.error||!r.data.session){const e=r.error?[r.error.status,r.error.message].filter(Boolean).join(" ").trim():"no session returned";throw new Error(`Token refresh failed (${e}). Your saved ATOMS session is no longer valid — re-run 'npx @atoms-tech/atoms-mcp login'.`)}const n=r.data.session;return await G({access_token:n.access_token,refresh_token:n.refresh_token,expires_at:Date.now()+1e3*(n.expires_in??3600),user_email:n.user?.email}),{access_token:n.access_token,refresh_token:n.refresh_token,user_id:n.user?.id??"",email:n.user?.email??""}}(t))}function Se(e){const t=e.split(".");if(3!==t.length)throw new Error("Invalid JWT format");const r=t[1].replace(/-/g,"+").replace(/_/g,"/").padEnd(t[1].length+(4-t[1].length%4)%4,"="),i=JSON.parse(Buffer.from(r,"base64").toString("utf-8"));if(!i.sub)throw new Error("JWT missing 'sub' claim");return i}I(be,{getValidToken:()=>je,readValidToken:()=>ve});var xe,ke,Ee,Ie,Ae,Re=E({"src/auth/refresh.ts"(){oe(),he(),we()}}),Oe={};async function ze(){if(xe)try{const e=await Q();e&&e.expires_at>Ae&&(process.stderr.write("[atoms-mcp] Credentials file refreshed elsewhere — rebuilding client.\n"),De())}catch{}if(xe&&Ie>Date.now()+6e4)return xe;xe&&process.stderr.write("[atoms-mcp] Token expiring, refreshing client...\n");const{access_token:e,user_id:t,email:r}=await je(),n=e.split(".");if(3===n.length)try{const e=JSON.parse(Buffer.from(n[1].replace(/-/g,"+").replace(/_/g,"/"),"base64").toString());Ie=1e3*(e.exp??0)}catch{Ie=Date.now()+36e5}try{const e=await Q();Ae=e?.expires_at??0}catch{Ae=0}const a=i.createClient(ue,_e,{global:{headers:{Authorization:`Bearer ${e}`}}});return ke=t,Ee=r,xe=a}function De(){xe=null,ke=null,Ee=null,Ie=0,Ae=0}function He(e){let t="";if(e instanceof Error)t=e.message;else if(e&&"object"==typeof e){const r=e;t="string"==typeof r.message?r.message:"string"==typeof r.code?r.code:String(e)}else null!=e&&(t=String(e));return/jwt\s*expired|invalid.?jwt|token.*(?:has\s+)?expired|jwt.*invalid|pgrst301/i.test(t)}async function Ue(e){try{return await e()}catch(t){if(!He(t))throw t;return process.stderr.write("[atoms-mcp] Data tier rejected JWT — invalidating client and retrying once.\n"),De(),await e()}}function Ce(){if(!ke)throw new Error("Not authenticated. Call getClient() first.");return ke}function qe(){return Ee??""}async function Te(e,t){const r=Ce(),{data:i,error:n}=await e.from("projects").select("org_id").eq("id",t).maybeSingle();if(n||!i)throw new Error(`Project '${t}' not found`);const{data:a,error:s}=await e.from("org_members").select("role").eq("user_id",r).eq("org_id",i.org_id).maybeSingle();if(s||!a){const{data:t}=await e.rpc("is_platform_admin");if(!0===t)return"admin";throw new Error("Not a member of this project's organization")}if("viewer"===a.role)throw new Error("VIEWER_ROLE");return a.role}async function Me(e,t){const r=Ce(),{data:i,error:n}=await e.from("projects").select("org_id, created_by").eq("id",t).maybeSingle();if(n||!i)throw new Error(`Project '${t}' not found`);const{data:a,error:s}=await e.from("org_members").select("role").eq("user_id",r).eq("org_id",i.org_id).maybeSingle();if(s||!a)throw new Error("Not a member of this project's organization");if("admin"===a.role)return"admin";if(i.created_by===r)return"owner";throw new Error("PROJECT_FIELD_ADMIN_OR_OWNER_REQUIRED")}I(Oe,{getClient:()=>ze,getUserEmail:()=>qe,getUserId:()=>Ce,invalidateClient:()=>De,isJwtExpiredError:()=>He,requireProjectFieldDefinitionAccess:()=>Me,requireWriteAccess:()=>Te,withJwtRetry:()=>Ue});var Pe,$e,Ne=E({"src/db/client.ts"(){Re(),oe(),we(),xe=null,ke=null,Ee=null,Ie=0,Ae=0}}),Le={};async function Fe(){const e=a.randomBytes(32).toString("base64url"),t=a.createHash("sha256").update(e).digest("base64url"),r=`http://localhost:${Pe}${$e}`,i=new s.URL(`${fe}/auth/mcp-consent`);return i.searchParams.set("redirect_uri",r),i.searchParams.set("code_challenge",t),i.searchParams.set("code_challenge_method","S256"),new Promise((t,r)=>{let a;function o(){clearTimeout(a)}const d=n.createServer(async(i,n)=>{const a=new s.URL(i.url??"/",`http://localhost:${Pe}`);if(a.pathname!==$e)return n.writeHead(404),void n.end("Not found");try{if("access_denied"===a.searchParams.get("error"))return n.writeHead(200,{"Content-Type":"text/html"}),n.end(Ve("Authorization was cancelled.")),o(),d.close(),void r(new Error("Authorization cancelled by user."));const i=a.searchParams.get("code");if(i){const a=await fetch(`${ue}/auth/v1/token?grant_type=pkce`,{method:"POST",headers:{"Content-Type":"application/json",apikey:_e},body:JSON.stringify({auth_code:i,code_verifier:e})}),s=await a.json();if(!a.ok||!s.access_token){const e=s.error_description??s.msg??"Unknown error";return n.writeHead(200,{"Content-Type":"text/html"}),n.end(Ve(`Code exchange failed: ${e}`)),o(),d.close(),void r(new Error(`Code exchange failed: ${e}`))}let c="authenticated";try{c=JSON.parse(Buffer.from(s.access_token.split(".")[1],"base64").toString()).email??c}catch{}const{createClient:l}=await import("@supabase/supabase-js"),m=l(ue,_e,{global:{headers:{Authorization:`Bearer ${s.access_token}`}}}),{data:p,error:u}=await m.from("org_members").select("org_id").limit(1);return u||!p||0===p.length?(n.writeHead(200,{"Content-Type":"text/html"}),n.end(Ve('No ATOMS account found for this Google account.<br><br>Please sign up at <a href="https://atoms.tech">atoms.tech</a> first, then run this login command again.')),o(),d.close(),void r(new Error("No ATOMS account found. Sign up at atoms.tech first."))):s.refresh_token?(await G({access_token:s.access_token,refresh_token:s.refresh_token,expires_at:Date.now()+1e3*(s.expires_in??3600),user_email:c}),n.writeHead(200,{"Content-Type":"text/html"}),n.end(We(c)),o(),d.close(),void t({email:c})):(n.writeHead(200,{"Content-Type":"text/html"}),n.end(Ve("Sign-in succeeded but no refresh token was issued, so the session would expire within the hour. This usually points to a Supabase Auth setting (refresh-token rotation or session policy). Please contact ATOMS support.")),o(),d.close(),void r(new Error("No refresh token issued by Supabase — cannot persist a durable session.")))}const s=a.searchParams.get("access_token"),c=a.searchParams.get("refresh_token"),l=parseInt(a.searchParams.get("expires_in")??"3600",10);s&&c?(await G({access_token:s,refresh_token:c,expires_at:Date.now()+1e3*l}),n.writeHead(200,{"Content-Type":"text/html"}),n.end(We("authenticated")),o(),d.close(),t({email:"authenticated"})):(n.writeHead(200,{"Content-Type":"text/html"}),n.end("<!DOCTYPE html>\n<html>\n<head><title>ATOMS MCP Login</title></head>\n<body>\n <h1>Completing login...</h1>\n <script>\n const hash = window.location.hash.substring(1);\n const params = new URLSearchParams(hash);\n const data = {\n access_token: params.get('access_token'),\n refresh_token: params.get('refresh_token'),\n expires_in: params.get('expires_in'),\n user_email: ''\n };\n if (data.access_token) {\n // Decode JWT to get email\n try {\n const payload = JSON.parse(atob(data.access_token.split('.')[1]));\n data.user_email = payload.email || '';\n } catch(e) {}\n fetch('/token', {\n method: 'POST',\n headers: { 'Content-Type': 'application/json' },\n body: JSON.stringify(data)\n }).then(() => {\n document.body.innerHTML = '<h1>Login successful! You can close this tab.</h1>';\n }).catch(() => {\n document.body.innerHTML = '<h1>Login failed. Please try again.</h1>';\n });\n } else {\n document.body.innerHTML = '<h1>Login failed — no tokens received.</h1>';\n }\n <\/script>\n</body>\n</html>"))}catch(e){n.writeHead(500),n.end("Authentication failed"),o(),d.close(),r(e)}});d.on("request",async(e,i)=>{if("POST"===e.method&&"/token"===e.url){let n="";e.on("data",e=>{n+=e.toString()}),e.on("end",async()=>{try{const e=JSON.parse(n);await G({access_token:e.access_token,refresh_token:e.refresh_token,expires_at:Date.now()+1e3*(e.expires_in??3600),user_email:e.user_email}),i.writeHead(200,{"Content-Type":"application/json"}),i.end(JSON.stringify({ok:!0})),o(),d.close(),t({email:e.user_email??"authenticated"})}catch(e){i.writeHead(500),i.end("Failed to store credentials"),o(),d.close(),r(e)}})}}),d.listen(Pe,"127.0.0.1",async()=>{process.stderr.write("\nOpening browser for ATOMS login...\n"),process.stderr.write(`If the browser doesn't open, visit:\n${i.toString()}\n\n`);try{const{default:e}=await import("open");await e(i.toString())}catch{process.stderr.write("Could not open browser automatically. Please open the URL above.\n")}}),a=setTimeout(()=>{d.close(),r(new Error("Login timed out after 60 seconds. Run 'npx @atoms-tech/atoms-mcp login' to try again."))},6e4)})}function We(e){return`<!DOCTYPE html>\n<html>\n<head>\n <title>ATOMS MCP — Authorized</title>\n <style>\n * { margin: 0; padding: 0; box-sizing: border-box; }\n body {\n font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', system-ui, sans-serif;\n background: #0a0a0a;\n color: #fafafa;\n display: flex;\n align-items: center;\n justify-content: center;\n min-height: 100vh;\n }\n .card {\n background: #171717;\n border: 1px solid #262626;\n border-radius: 16px;\n padding: 48px;\n max-width: 480px;\n width: 100%;\n text-align: center;\n }\n .icon {\n width: 56px;\n height: 56px;\n background: #052e16;\n border-radius: 50%;\n display: flex;\n align-items: center;\n justify-content: center;\n margin: 0 auto 24px;\n }\n .icon svg { width: 28px; height: 28px; }\n h1 {\n font-size: 22px;\n font-weight: 600;\n margin-bottom: 8px;\n color: #22c55e;\n }\n .email {\n font-size: 14px;\n color: #a3a3a3;\n margin-bottom: 32px;\n }\n .permissions {\n text-align: left;\n background: #0a0a0a;\n border: 1px solid #262626;\n border-radius: 12px;\n padding: 20px;\n margin-bottom: 24px;\n }\n .permissions h3 {\n font-size: 12px;\n font-weight: 600;\n color: #737373;\n text-transform: uppercase;\n letter-spacing: 0.05em;\n margin-bottom: 12px;\n }\n .perm-item {\n display: flex;\n align-items: center;\n gap: 10px;\n padding: 6px 0;\n font-size: 14px;\n color: #d4d4d4;\n }\n .perm-item .dot {\n width: 6px;\n height: 6px;\n background: #22c55e;\n border-radius: 50%;\n flex-shrink: 0;\n }\n .closing {\n font-size: 13px;\n color: #525252;\n }\n .closing span { color: #a3a3a3; font-variant-numeric: tabular-nums; }\n </style>\n</head>\n<body>\n <div class="card">\n <div class="icon">\n <svg fill="none" viewBox="0 0 24 24" stroke="#22c55e" stroke-width="2.5">\n <path stroke-linecap="round" stroke-linejoin="round" d="M5 13l4 4L19 7"/>\n </svg>\n </div>\n <h1>Authorization Granted</h1>\n <p class="email">${e}</p>\n\n <div class="permissions">\n <h3>ATOMS MCP can now</h3>\n <div class="perm-item"><span class="dot"></span> Read your projects and requirements</div>\n <div class="perm-item"><span class="dot"></span> Create and edit requirements and test cases</div>\n <div class="perm-item"><span class="dot"></span> Record test results (pass/fail)</div>\n <div class="perm-item"><span class="dot"></span> Manage traceability relationships</div>\n <div class="perm-item"><span class="dot"></span> Export coverage reports and diagrams</div>\n </div>\n\n <p class="closing">This tab will close in <span id="countdown">5</span>s</p>\n </div>\n\n <script>\n let seconds = 5;\n const el = document.getElementById('countdown');\n const timer = setInterval(() => {\n seconds--;\n el.textContent = seconds;\n if (seconds <= 0) {\n clearInterval(timer);\n window.close();\n // If window.close() is blocked (not opened by script), update message\n setTimeout(() => {\n document.querySelector('.closing').textContent = 'You can close this tab now.';\n }, 500);\n }\n }, 1000);\n <\/script>\n</body>\n</html>`}function Ve(e){return`<!DOCTYPE html>\n<html>\n<head>\n <title>ATOMS MCP — Failed</title>\n <style>\n * { margin: 0; padding: 0; box-sizing: border-box; }\n body {\n font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', system-ui, sans-serif;\n background: #0a0a0a;\n color: #fafafa;\n display: flex;\n align-items: center;\n justify-content: center;\n min-height: 100vh;\n }\n .card {\n background: #171717;\n border: 1px solid #262626;\n border-radius: 16px;\n padding: 48px;\n max-width: 480px;\n width: 100%;\n text-align: center;\n }\n .icon {\n width: 56px;\n height: 56px;\n background: #450a0a;\n border-radius: 50%;\n display: flex;\n align-items: center;\n justify-content: center;\n margin: 0 auto 24px;\n }\n .icon svg { width: 28px; height: 28px; }\n h1 { font-size: 22px; font-weight: 600; margin-bottom: 16px; color: #ef4444; }\n .reason { font-size: 14px; color: #a3a3a3; line-height: 1.6; }\n .reason a { color: #7c3aed; text-decoration: underline; }\n </style>\n</head>\n<body>\n <div class="card">\n <div class="icon">\n <svg fill="none" viewBox="0 0 24 24" stroke="#ef4444" stroke-width="2.5">\n <path stroke-linecap="round" stroke-linejoin="round" d="M6 18L18 6M6 6l12 12"/>\n </svg>\n </div>\n <h1>Authorization Failed</h1>\n <p class="reason">${e}</p>\n </div>\n</body>\n</html>`}I(Le,{login:()=>Fe});var Be,Je,Qe,Ge,Ye=E({"src/auth/login.ts"(){oe(),we(),Pe=19275,$e="/callback"}});function Ke(e,t=0){if(t>5)return"[depth-limit]";if("string"==typeof e){for(const t of Qe)if(t.test(e.trim()))return"[redacted]";return e.length>Ge?e.slice(0,Ge)+"…":e}if(Array.isArray(e))return e.slice(0,20).map(e=>Ke(e,t+1));if(null!==e&&"object"==typeof e){const r={};for(const[i,n]of Object.entries(e)){const e=i.toLowerCase();Be.has(e)?r[i]="[redacted]":Je.has(e)?r[i]="string"==typeof n?"[content]":Ke(n,t+1):r[i]=Ke(n,t+1)}return r}return e}function Ze(e){return Ke(e)}var Xe,et,tt,rt,it,nt=E({"src/middleware/audit.ts"(){Be=new Set(["access_token","refresh_token","password","api_key","secret","token","authorization","credential","credentials","private_key"]),Je=new Set(["body","description","content","notes","summary","title","system_prompt","prompt"]),Qe=[/^[^\s@]+@[^\s@]+\.[^\s@]+$/,/^bearer\s+\S+$/i,/^(sk|pk|npm|gh|glpat|xoxb|xoxp|rk|SG\.)[-_][A-Za-z0-9_-]{16,}/,/^eyJ[A-Za-z0-9_-]+\.eyJ[A-Za-z0-9_-]+\.[A-Za-z0-9_-]+$/],Ge=200}}),at=E({"src/middleware/rate-limiter.ts"(){Xe=60,et=6e4}});function st(){const e=process.env.ATOMS_MCP_PROJECT_ID?.trim();return e?tt.test(e)?e:(rt||(process.stderr.write(`[atoms-mcp] WARNING: ATOMS_MCP_PROJECT_ID="${e.slice(0,50)}" is not a valid UUID — scope ignored.\n`),rt=!0),null):null}var ot,dt=E({"src/middleware/project-scope.ts"(){tt=/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i,rt=!1,it=class extends Error{expectedProjectId;receivedProjectId;constructor(e,t){super("Tool call rejected: project_id is outside the configured ATOMS_MCP_PROJECT_ID scope."),this.name="ProjectScopeError",this.expectedProjectId=e,this.receivedProjectId=t}}}});function ct(e){const t=function(e){return e.trim().toLowerCase().replace(/[^a-z0-9]+/g,"_").replace(/^_+|_+$/g,"")}(e??"");return t?t.includes("cursor")?"cursor":t.includes("copilot")?"copilot":t.includes("claude")?ot:t:ot}var lt,mt,pt,ut,_t,ft,ht,gt,yt=E({"src/core/client-identity.ts"(){ot="claude_desktop"}}),wt=E({"src/core/timestamps.ts"(){lt=o.z.string().datetime({offset:!0})}}),bt=E({"src/core/errors.ts"(){}}),vt={};function jt(e,t=pt){if("string"!=typeof e)return"";const r=e.replace(_t,"").replace(ft,"");return r.length<=t?r:r.slice(0,t)+"..."}function St(e){return"string"!=typeof e?"":e.trim().toLowerCase().replace(/\s+/g,"-").replace(/[^a-z0-9-]/g,"").replace(/-+/g,"-").replace(/^-|-$/g,"")}function xt(e,t){return{status:"success",data:e,...t?{meta:t}:{}}}function kt(e,t,r){return{total_count:e,limit:t,offset:r,has_more:r+t<e}}function Et(e,t){return{status:"error",message:e,next_steps:t}}function It(e,t){return Et(`${e} '${jt(t)}' not found`,[`Verify the ${e.toLowerCase()} ID is correct`,"Use atoms_list_items or atoms_search to find valid IDs"])}function At(e){return Et(`${e} role cannot modify project data`,["Contact your org admin to upgrade your role to editor","Use read-only tools (atoms_list_items, atoms_get_item, atoms_search) instead"])}function Rt(e){return Et(`Validation error: ${jt(e,ut)}`,["Check the parameter types and constraints in the tool description","Ensure all required parameters are provided"])}function Ot(){return Et("Not authenticated. 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Bt(xt({id:n.id,type:n.type,title:n.title,summary:n.data?.summary,body:n.data?.body,tags:n.data?.tags??{domains:[]},ownership:n.data?.ownership??{primary:null,additional:[]},relationships:a,links:n.data?.links??[],fields:(t=n.data?.fields,!t||"object"!=typeof t||Array.isArray(t)?{}:Object.fromEntries(Object.entries(t).filter(e=>"string"==typeof e[1]))),status:n.data?.status,..."test-case"===n.type?{latest_result:s[0]?.result??"not-run",test_results:s}:{},metadata:{created_at:n.created_at,created_by:n.created_by,updated_at:n.updated_at,updated_by:n.updated_by,source_id:n.data?.metadata?.source_id}}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Jt(Ot()):Jt(Lt(e instanceof Error?e.message:String(e)))}var t}I(hr,{getItemHandler:()=>yr});var wr=E({"src/tools/get-item.ts"(){Ne(),dr(),Gt(),_r=["point","release_id","build","environment","tooling","step_results"]}}),br={};async function vr(e){try{const t=await ze();let r,i,n=null;try{n=await 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ze(),{access_token:r}=await je(),{items:i,totalCount:n}=await async function(e,t,r,i){const{ATOMS_SUPABASE_URL:n,ATOMS_SUPABASE_ANON_KEY:a}=await Promise.resolve().then(()=>(we(),ge)),s=await fetch(`${n}/functions/v1/embed`,{method:"POST",headers:{"Content-Type":"application/json",Authorization:`Bearer ${i.accessToken}`,apikey:a},body:JSON.stringify({input:r})});if(!s.ok)throw new Error(`Embed function failed: ${s.status}`);const{embedding:o}=await s.json(),{data:d,error:c}=await e.rpc("semantic_search",{query_embedding:o,p_project_id:t,match_threshold:.3,match_count:i.limit,p_type:i.type||null});if(c)throw new Error(c.message);return{items:d??[],totalCount:(d??[]).length,method:"semantic"}}(t,e.project_id,e.query,{type:e.type,limit:e.limit,accessToken:r});return Bt(xt(i.map(e=>({id:e.id,title:e.title,type:e.type,status:e.data?.status,domains:e.data?.tags?.domains??[],level:e.data?.tags?.level})),kt(n,e.limit,0)))}catch(e){return e instanceof Error&&e.message.includes("Not 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Jt($t(n));const{data:a,error:s}=await t.from("verification_status").select("requirement_id, state, stale, points_total, points_run").eq("project_id",e.project_id).eq("release_id",r.id);if(s)return Jt(Lt(s.message));const o=(a??[]).slice().sort((e,t)=>e.requirement_id<t.requirement_id?-1:e.requirement_id>t.requirement_id?1:0),d={release:{id:r.id,version:r.release_version,status:r.release_status},readiness:i??{},requirements:o,...0===o.length?{hint:"projection empty; an admin may need to run rebuild_verification_from_runs for this project"}:{}};if(e.include_gaps){const{data:i,error:n}=await t.rpc("verification_notrun_points",{p_project_id:e.project_id,p_release_id:r.id});if(n)return Jt($t(n));d.gaps=i??[]}return Bt(xt(d))}catch(e){return Jt($t(e))}}I(Or,{verificationStatusHandler:()=>zr});var Dr=E({"src/tools/verification-status.ts"(){Ne(),dr(),Gt(),Ar=Et("This project has no current formal Release.",["Promote a locked baseline to a Release first (Snapshots view in the app)","Or pass 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null!==r?{updated_fields:u,updatedData:p,itemType:o.type,capturedSg:r}:{updated_fields:u,updatedData:p,itemType:o.type,capturedUnknown:!0}}return{updated_fields:u,updatedData:p,itemType:o.type}};if(e.updates&&Array.isArray(e.updates)){const t=crypto.randomUUID(),r=!0===e.continue_on_error,n=[],a=[];for(const s of e.updates){const{updated_fields:o,capturedSg:d,capturedUnknown:c,error:l}=await i(s.item_id,s,t,e.reason);if(l){if(Nt(l))return Jt($t(l));if(!r){const e=l instanceof Error?l.message:String("object"==typeof l&&l&&"message"in l?l.message??"":l);return Jt(Rt(`Batch stopped at "${s.item_id}": ${e}. ${n.length} item(s) already updated.`))}a.push({item_id:s.item_id,error:String(l)})}else void 0!==d?n.push(Fi(s.item_id,d)):c?n.push(Wi(s.item_id)):n.push({id:s.item_id,updated_fields:o})}return Bt(xt({batch_id:t,updated:n.length,results:!1===e.echo?void 0:n,errors:a}))}if(!e.item_id)return Jt(Rt("Provide either item_id (single) or updates[] (array 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Qi,Gi,Yi=E({"src/tools/update-item.ts"(){Ne(),dr(),is(),Gt(),di(),Vi(),vi()}});function Ki(e){const t=process.env.ATOMS_MCP_REQUIRE_CONFIRMATION?.trim();if(t){const r=t.toLowerCase();if("1"===r||"true"===r||"all"===r)return!0;if(t.split(",").map(e=>e.trim()).filter(Boolean).includes(e))return!0}return!!P().require_confirmation_for.includes(e)}function Zi(e,t=Qi){const r=Date.now()+t,i={...e,exp:r},n=Buffer.from(JSON.stringify(i)).toString("base64url");return{token:`${n}.${S.default.createHmac("sha256",Gi).update(n).digest("base64url")}`,expires_at:new Date(r).toISOString(),expires_in_seconds:Math.round(t/1e3)}}function Xi(e,t){if("string"!=typeof e||!e.includes("."))return{valid:!1,reason:"Token format invalid"};const[r,i]=e.split(".");if(!r||!i)return{valid:!1,reason:"Token format invalid"};const n=S.default.createHmac("sha256",Gi).update(r).digest("base64url"),a=Buffer.from(i,"utf8"),s=Buffer.from(n,"utf8");if(a.length!==s.length||!S.default.timingSafeEqual(a,s))return{valid:!1,reason:"Token signature invalid"};let o;try{o=JSON.parse(Buffer.from(r,"base64url").toString("utf8"))}catch{return{valid:!1,reason:"Token payload malformed"}}return"number"!=typeof o.exp||o.exp<Date.now()?{valid:!1,reason:"Token expired"}:o.tool!==t.tool?{valid:!1,reason:"Token issued for a different tool"}:o.project_id!==t.project_id?{valid:!1,reason:"Token issued for a different project"}:o.target!==t.target?{valid:!1,reason:"Token issued for a different target"}:{valid:!0}}function en(e){if(Array.isArray(e))return e.map(en);if(null!==e&&"object"==typeof e){const t={};for(const r of Object.keys(e).sort())t[r]=en(e[r]);return t}return e}function tn(e){const t=JSON.stringify(en(e));return S.default.createHash("sha256").update(t).digest("base64url").slice(0,16)}var rn,nn=E({"src/middleware/confirmation.ts"(){$(),Qi=6e4,Gi=(()=>{const e=process.env.ATOMS_MCP_CONFIRMATION_SECRET;return e&&e.length>=16?e:S.default.randomBytes(32).toString("base64url")})()}}),an={};async function sn(e){try{const t=await ze(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Jt(At("Viewer"));throw e}const i=await async function(e,t,r){const{data:i,error:n}=await e.from("items").select("*").eq("id",r).eq("project_id",t).maybeSingle();if(n)throw new Error(n.message);return i}(t,e.project_id,e.item_id);if(!i)return Jt(It("Item",e.item_id));if(i.deleted_at)return Jt(Rt(`Item ${e.item_id} is already deleted`));if(Ki(rn)){const t={tool:rn,project_id:e.project_id,target:e.item_id};if(!e.confirmation_token){const r=Zi(t);return Bt(xt({status:"confirmation_required",preview:{id:e.item_id,title:i.title,type:i.type,would_soft_delete:!0},confirmation_token:r.token,expires_at:r.expires_at,expires_in_seconds:r.expires_in_seconds,message:`Re-call atoms_delete_item with the same project_id, item_id, and confirmation_token within ${r.expires_in_seconds}s to execute.`}))}const r=Xi(e.confirmation_token,t);if(!r.valid)return Jt(Rt(`confirmation_token rejected: ${r.reason}`))}const{error:n}=await t.rpc("soft_delete_item_with_revision",{p_item_id:e.item_id,p_project_id:e.project_id,p_user_id:r,p_expected_updated_at:i.updated_at,p_event_source:"mcp",p_actor:ts(),p_session_id:es()});if(n)throw new Error(n.message);return Bt(xt({id:e.item_id,title:i.title,type:i.type,deleted:!0,message:`Item ${e.item_id} soft-deleted. It can still be found in audit logs.`}))}catch(e){return Jt($t(e))}}I(an,{deleteItemHandler:()=>sn});var on=E({"src/tools/delete-item.ts"(){Ne(),dr(),is(),nn(),Gt(),rn="atoms_delete_item"}}),dn={};async function cn(e){try{const t=await ze(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Jt(At("Viewer"));throw e}const{data:i,error:n}=await t.from("items").select("*").eq("id",e.item_id).eq("project_id",e.project_id).maybeSingle();if(n)throw new Error(n.message);if(!i)return Jt(It("Item",e.item_id));if(!i.deleted_at)return Jt(Et(`Item ${e.item_id} is not deleted and cannot be restored.`,["Use atoms_get_item to view the current item state","Use atoms_delete_item first if you intended to delete it"]));const{error:a}=await t.rpc("save_item_with_revision",{p_item_id:e.item_id,p_project_id:e.project_id,p_type:i.type,p_title:i.title,p_data:i.data,p_user_id:r,p_event_source:"restore",p_event_session_id:es()??null,p_diff_summary:{changed_fields:["deleted_at"],restored:!0},p_expected_updated_at:i.updated_at});if(a)throw new Error(a.message);const{error:s}=await t.rpc("repair_live_item_relationships_from_jsonb",{p_project_id:e.project_id,p_item_id:e.item_id});if(s)throw new Error(`Relationship repair failed: ${s.message}`);return await t.from("change_history").insert({item_id:e.item_id,project_id:e.project_id,changed_by:r,event_type:"restored",old_data:null,new_data:i.data,actor:ts(),session_id:es()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),Bt(xt({id:e.item_id,title:i.title,type:i.type,restored:!0,message:`Item ${e.item_id} restored successfully.`}))}catch(e){return Jt($t(e))}}I(dn,{restoreItemHandler:()=>cn});var ln=E({"src/tools/restore-item.ts"(){Ne(),is(),Gt()}}),mn={};async function pn(e){try{const t=await ze(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Jt(At("Viewer"));throw e}const i=async(i,n,a)=>{const s=await er(t,e.project_id,i.from_id);if(!s)throw new Error(`Item "${i.from_id}" not found`);const o=await er(t,e.project_id,i.to_id);if(!o)throw new Error(`Item "${i.to_id}" not found`);const{error:d}=await t.rpc("apply_link_change",{p_project_id:e.project_id,p_from_id:i.from_id,p_to_id:i.to_id,p_type:i.type,p_action:i.action,p_user_id:r,p_event_source:"mcp",p_expected_from_updated_at:i.expected_from_updated_at??s.updated_at,p_expected_to_updated_at:i.expected_to_updated_at??o.updated_at});if(d)throw new Error(d.message);const c={item_id:i.from_id,project_id:e.project_id,changed_by:r,event_type:"updated",old_data:null,new_data:{relationship_change:{action:i.action,type:i.type,from:i.from_id,to:i.to_id}},actor:ts(),session_id:es()};n&&(c.batch_id=n),a&&(c.reason=a),await t.from("change_history").insert(c).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)})};if(e.operations&&Array.isArray(e.operations)){for(const t of e.operations)if(t.from_id===t.to_id)return Jt(Rt(`Self-reference in batch: "${t.from_id}"`));const r=[...new Set(e.operations.flatMap(e=>[e.from_id,e.to_id]))],{data:n}=await t.from("items").select("id").eq("project_id",e.project_id).is("deleted_at",null).in("id",r),a=new Set((n??[]).map(e=>e.id)),s=r.filter(e=>!a.has(e));if(s.length>0)return Jt(It("Items",s.join(", ")));const{data:o}=await t.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id),d=new Map;for(const e of o??[])"parent"===e.type&&(d.has(e.from_id)||d.set(e.from_id,new Set),d.get(e.from_id).add(e.to_id));for(const t of e.operations){if("parent"!==t.type&&"child"!==t.type)continue;const[e,r]="parent"===t.type?[t.from_id,t.to_id]:[t.to_id,t.from_id];"remove"===t.action?d.get(e)?.delete(r):(d.has(e)||d.set(e,new Set),d.get(e).add(r))}const c=0,l=1,m=2,p=new Map,u=new Set;for(const[e,t]of d){u.add(e);for(const e of t)u.add(e)}const _=e=>{if((p.get(e)??c)!==c)return null;const t=[],r=[],i=e=>{p.set(e,l),r.push(e),t.push({node:e,parents:[...d.get(e)??[]],idx:0})};for(i(e);t.length>0;){const e=t[t.length-1];if(e.idx>=e.parents.length){p.set(e.node,m),r.pop(),t.pop();continue}const n=e.parents[e.idx];e.idx++;const a=p.get(n)??c;if(a===l){const e=r.indexOf(n);return[...r.slice(e),n]}a!==m&&i(n)}return null};for(const e of u){const t=_(e);if(t)return Jt(Rt(`Batch would create a cycle: ${t.join(" -> ")}. No changes applied.`))}const f=crypto.randomUUID(),h=e.operations.filter(e=>"remove"===e.action),g=e.operations.filter(e=>"add"===e.action);for(const t of[...h,...g])await i(t,f,e.reason);return Bt(xt({batch_id:f,processed:e.operations.length,operations:!1===e.echo?void 0:e.operations}))}return e.from_id&&e.to_id&&e.type&&e.action?e.from_id===e.to_id?Jt(Rt("Cannot create a relationship between an item and itself")):(await i({action:e.action,from_id:e.from_id,to_id:e.to_id,type:e.type,expected_from_updated_at:e.expected_from_updated_at,expected_to_updated_at:e.expected_to_updated_at},void 0,e.reason),!1===e.echo?Bt(xt({action:e.action,from_id:e.from_id,to_id:e.to_id})):Bt(xt({action:e.action,type:e.type,from_id:e.from_id,to_id:e.to_id,message:`Relationship ${"add"===e.action?"added":"removed"}: ${e.from_id} --[${e.type}]--\x3e ${e.to_id}`}))):Jt(Rt("Provide (from_id, to_id, type, action) for single-op or operations[] for batch."))}catch(e){return Jt($t(e))}}I(mn,{linkItemsHandler:()=>pn});var un=E({"src/tools/link-items.ts"(){Ne(),dr(),is(),Gt()}}),_n=E({"src/core/bulk-parent-links.ts"(){}}),fn={};function hn(e){return new Set(["22023","23503","23505","23514"]).has(e.code??"")}async function gn(e){try{if(!e.items||0===e.items.length)return Jt(Rt("items array must contain at least 1 item"));if(e.items.length>100)return Jt(Rt(`Maximum 100 items per call (received ${e.items.length}). Split into multiple calls.`));const t=await ze(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Jt(At("Viewer"));throw e}const i=await async function(e,t,r){const{data:i,error:n}=await e.from("metadata").select("domains, function_tags").eq("project_id",t).maybeSingle();if(n)throw new Error(`metadata read failed: ${n.message}`);const a=i?.domains??[],s=hi(i?.function_tags),o=a.length>0?new Set(a.map(St).filter(e=>e.length>0)):null,d=tn(a.map(St).filter(e=>e.length>0).sort()),c=[],l=new Set,m={};for(let e=0;e<r.length;e++){const t=r[e];m[t.type]=(m[t.type]??0)+1;const i=(t.domains??[]).map(St).filter(e=>e.length>0);if(0===i.length)continue;const n=gi(i,s,St);if(n.length>0){l.add(e),c.push({index:e,title:t.title,error:yi(n)});continue}if(!o)continue;const d=i.filter(e=>!o.has(e));d.length>0&&(l.add(e),c.push({index:e,title:t.title,error:`Unknown domain${d.length>1?"s":""}: ${d.join(", ")}. Registered: ${a.join(", ")}.`}))}return{registeredDomains:a,registeredDomainHash:d,invalidDomainIndexes:l,errors:c,typeBreakdown:m}}(t,e.project_id,e.items);if(Ki("atoms_bulk_import")){const t={tool:"atoms_bulk_import",project_id:e.project_id,target:tn({items:e.items,registered_domain_hash:i.registeredDomainHash})};if(!e.confirmation_token){const r=Zi(t);return Bt(xt({status:"confirmation_required",preview:{total_items:e.items.length,by_type:i.typeBreakdown,sample_titles:e.items.slice(0,5).map(e=>e.title),would_fail:i.errors.length>0,errors:i.errors,registered_domain_hash:i.registeredDomainHash},confirmation_token:r.token,expires_at:r.expires_at,expires_in_seconds:r.expires_in_seconds,message:`Re-call atoms_bulk_import with the same project_id, items array, and confirmation_token within ${r.expires_in_seconds}s to execute. 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Bt(xt({created:0,items:[],errors:o}));const m=[],p=new Map;for(const{itemId:t,input:i,sanitizedDomains:a,sanitizedLevel:s}of d){const o={id:t,type:i.type,title:i.title,summary:i.summary,body:i.body,tags:{domains:a,level:s??""},ownership:{primary:null,additional:[]},relationships:{parents:i.parent_id?[i.parent_id]:[],children:[],related:[]},links:[],metadata:{created_at:n,created_by:r,updated_at:n,updated_by:r}};p.set(t,o),m.push({id:t,project_id:e.project_id,type:i.type,title:i.title,data:o,created_by:r,updated_by:r})}const u=m.map(e=>({id:e.id,type:e.type,title:e.title,data:e.data})),{error:_}=await t.rpc("bulk_save_items_with_revisions",{p_project_id:e.project_id,p_items:u,p_user_id:r,p_event_source:"mcp"});if(_&&hn(_))for(const{itemId:i,input:n,index:c}of d){const d=m.find(e=>e.id===i);if(!d)continue;const{error:l}=await t.rpc("save_item_with_revision",{p_item_id:d.id,p_project_id:e.project_id,p_type:d.type,p_title:d.title,p_data:d.data,p_user_id:r,p_event_source:"mcp",p_event_session_id:a,p_diff_summary:null});l?o.push({index:c,title:n.title,error:l.message}):s.push({id:i,title:n.title,type:n.type})}else{if(_)throw _;for(const{itemId:e,input:t}of d)s.push({id:e,title:t.title,type:t.type})}const f=d.filter(({input:e})=>e.parent_id).filter(({itemId:e})=>s.some(t=>t.id===e)).map(({itemId:t,input:r})=>({from_id:t,to_id:r.parent_id,type:"parent",project_id:e.project_id}));await async function(e){for(const t of e.links){const{error:r}=await e.client.rpc("apply_link_change",{p_project_id:e.projectId,p_from_id:t.from,p_to_id:t.to,p_type:"parent",p_action:"add",p_user_id:e.userId,p_event_source:"mcp"});r&&e.warn(`bulk parent link sync failed for ${t.to}: ${r.message??"unknown 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Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Jt(At("Viewer"));throw e}const n=await er(t,e.project_id,e.item_id);if(!n)return Jt(It("Item",e.item_id));if("test-case"!==n.type)return Jt(Rt(`Item '${e.item_id}' is a ${n.type}, not a test-case`));const a=(e.asset??"").trim(),s=(new Date).toISOString(),{data:o,error:d}=await t.rpc("record_test_results_bulk",{p_project_id:e.project_id,p_item_id:e.item_id,p_run_by:i||r,p_actor_user_id:r,p_results:[{result:e.result,note:e.note,asset:a||void 0,date:s,point:e.point,release_id:e.release_id,build:e.build,environment:e.environment,tooling:e.tooling,steps_rev:e.steps_rev,step_results:e.step_results}]});if(d)throw new Error(d.message);const c=Array.isArray(o)?o[0]:o?.[0];await t.from("change_history").insert({item_id:e.item_id,project_id:e.project_id,changed_by:r,event_type:"test_result_recorded",old_data:null,new_data:{result:e.result,run_at:s,note:e.note,asset:a||null},actor:ts(),session_id:es()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)});const l=a?` (asset: ${a})`:"";return Bt(xt({item_id:e.item_id,result:e.result,run_at:s,run_by:i||r,note:e.note??null,asset:a||null,asset_id:c?.asset_id??null,asset_created:c?.asset_created??!1,message:`Test result '${e.result}' recorded for ${e.item_id}${l}`}))}catch(e){return Jt($t(e))}}I(wn,{recordTestResultHandler:()=>bn});var vn=E({"src/tools/record-test-result.ts"(){Ne(),dr(),is(),Gt()}}),jn={};async function Sn(e){try{const t=await ze(),r=Ce(),i=qe();if(!Array.isArray(e.results)||0===e.results.length)return Jt(Rt("results must be a non-empty array"));if(e.results.length>100)return Jt(Rt(`results must have at most 100 entries (got 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Jt($t(e))}}I(jn,{recordTestResultsBulkHandler:()=>Sn});var xn,kn,En,In,An=E({"src/tools/record-test-results-bulk.ts"(){Ne(),dr(),is(),Gt()}});function Rn(e){return Math.min(Math.max(e??5,1),10)}var On=E({"src/core/trace-graph.ts"(){xn=200,kn=new Set(["parent","verifies","mitigated_by"]),En=new Set(["child","verified_by","mitigates"]),In={parent:"child",child:"parent",verifies:"verified_by",verified_by:"verifies",mitigated_by:"mitigates",mitigates:"mitigated_by",related:"related"}}}),zn={};async function Dn(e){try{const t=Rn(e.depth),r=await ze(),i=await er(r,e.project_id,e.item_id);if(!i)return Jt(It("Item",e.item_id));const{data:n,error:a}=await r.from("items").select("id, title, type, data").eq("project_id",e.project_id).is("deleted_at",null);if(a)throw new Error(a.message);const{data:s,error:o}=await r.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(o)throw new Error(o.message);const d=sr(n??[],s??[]);return Bt(xt(function(e){const t=Rn(e.depth),r=e.relationshipTypes?.length?new Set(e.relationshipTypes):null,i=new Map(e.items.map(e=>[e.id,e]));i.has(e.rootItemId)||i.set(e.rootItemId,e.rootItem);const n=new Map,a=(e,t,r)=>{n.has(e)||n.set(e,[]),n.get(e).push({neighbor:t,relType:r})};for(const t of e.relationships){const i=t.type;if(("upstream"===e.direction||"both"===e.direction)&&(!kn.has(i)||r&&!r.has(i)||a(t.from_id,t.to_id,i),En.has(i))){const e=In[i]??i;r&&!r.has(e)||a(t.to_id,t.from_id,e)}if(("downstream"===e.direction||"both"===e.direction)&&(!En.has(i)||r&&!r.has(i)||a(t.from_id,t.to_id,i),kn.has(i))){const e=In[i]??i;r&&!r.has(e)||a(t.to_id,t.from_id,e)}"related"!==i||r&&!r.has("related")||(a(t.from_id,t.to_id,"related"),a(t.to_id,t.from_id,"related"))}const s=new Set([e.rootItemId]),o=[],d=[],c=[];for(const t of n.get(e.rootItemId)??[])c.push({id:t.neighbor,depth:1,relType:t.relType,from:e.rootItemId});for(;c.length>0&&o.length<xn;){const{id:e,depth:r,relType:a,from:l}=c.shift();if(s.has(e)||r>t)continue;s.add(e);const m=i.get(e);if(m&&(o.push({id:e,title:m.title,type:m.type,relationship:a,depth:r,from:l}),d.push({from:l,to:e,type:a}),r<t))for(const t of n.get(e)??[])s.has(t.neighbor)||c.push({id:t.neighbor,depth:r+1,relType:t.relType,from:e})}const l={id:e.rootItemId,title:e.rootItem.title,type:e.rootItem.type,relationship:"root",depth:0,from:e.rootItemId};return{root:e.rootItemId,project_id:e.projectId,direction:e.direction,depth_limit:t,items:[l,...o],edges:d,total_count:o.length+1,...o.length>=xn?{truncated:!0,truncation_message:`Results capped at ${xn} items. 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Use letters, digits, underscores; must start with letter or underscore.`));const a=e.variables.map(e=>e.name),s=a.filter((e,t)=>a.indexOf(e)!==t);if(s.length>0)return Jt(Rt(`Duplicate names in batch: ${[...new Set(s)].join(", ")}`));const{data:o}=await t.from("project_variables").select("name").eq("project_id",e.project_id).in("name",a),d=(o??[]).map(e=>e.name);if(d.length>0)return Jt(Rt(`Variable(s) already exist: ${d.join(", ")}. Remove them from the batch or use atoms_update_variable to change values.`));const c=e.variables.map(t=>({project_id:e.project_id,name:t.name,value:t.value,unit:t.unit??null,description:t.description??null,created_by:r,updated_by:r})),l=await async function(e,t,r,i){const{data:n,error:a}=await e.rpc("bulk_save_variables_with_revisions",{p_project_id:t,p_variables:r,p_user_id:i,p_event_source:"mcp"});if(a)throw new Error(a.message);return n??[]}(t,e.project_id,c,r);return Bt(xt({batch_id:crypto.randomUUID(),created:(l??[]).length,variables:!1===e.echo?(l??[]).map(e=>({name:e.name})):l??[],message:`${(l??[]).length} variable(s) created. Reference them as {name} in requirement bodies.`}))}if(!e.name||!e.value)return Jt(Rt("Provide either (name, value) for single variable or variables[] for batch."));if(!i.test(e.name))return Jt(Rt(`Variable name "${e.name}" is invalid. Use letters, digits, and underscores only; must start with a letter or underscore.`));const{data:n}=await t.from("project_variables").select("name").eq("project_id",e.project_id).eq("name",e.name).maybeSingle();if(n)return Jt(Rt(`Variable "${e.name}" already exists in this project.`));const a=await $n(t,{project_id:e.project_id,name:e.name,value:e.value,unit:e.unit??null,description:e.description??null},r,"mcp");return!1===e.echo?Bt(xt({name:e.name})):Bt(xt({variable:a,message:`Variable "${e.name}" created. Reference it in requirement bodies as {${e.name}}.`}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Jt(Ot()):Jt(Lt(e instanceof Error?e.message:String(e)))}}async function Vn(e){try{const t=await ze(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Jt(At("Viewer"));throw e}const{data:i}=await t.from("project_variables").select("id").eq("project_id",e.project_id).eq("name",e.name).maybeSingle();if(!i)return Jt(It("Variable",e.name));const{data:n}=await t.from("items").select("id").eq("project_id",e.project_id).is("deleted_at",null).filter("data->>body","ilike",`%{${e.name}}%`),a=(n??[]).length;if(a>0&&!e.force)return Jt(Rt(`Variable "${e.name}" is referenced in ${a} item${a>1?"s":""}. Use force=true to delete anyway, or remove all {${e.name}} references first.`));if(Ki("atoms_delete_variable")){const t={tool:"atoms_delete_variable",project_id:e.project_id,target:e.name};if(!e.confirmation_token){const r=Zi(t);return Bt(xt({status:"confirmation_required",preview:{variable_name:e.name,referenced_by_items:a,would_orphan_references:a>0},confirmation_token:r.token,expires_at:r.expires_at,expires_in_seconds:r.expires_in_seconds,message:`Re-call atoms_delete_variable with the same project_id, name, and confirmation_token within ${r.expires_in_seconds}s to execute.`}))}const r=Xi(e.confirmation_token,t);if(!r.valid)return Jt(Rt(`confirmation_token rejected: ${r.reason}`))}const s=await async function(e,t,r,i){const{data:n,error:a}=await e.rpc("delete_variable_with_revision",{p_project_id:t,p_variable_id:r,p_user_id:i,p_event_source:"mcp"});if(a)throw new Error(a.message);return Boolean(n)}(t,e.project_id,i.id,r);return s?Bt(xt({deleted:!0,name:e.name,referenced_by_items:a,warning:a>0?`${a} item${a>1?"s":""} still contain {${e.name}} — those references are now unresolved.`:void 0})):Jt(It("Variable",e.name))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Jt(Ot()):Jt(Lt(e instanceof Error?e.message:String(e)))}}I(Tn,{createVariableHandler:()=>Wn,deleteVariableHandler:()=>Vn,getVariableHandler:()=>Ln,listVariablesHandler:()=>Nn,updateVariableHandler:()=>Fn});var Bn=E({"src/tools/variables.ts"(){Ne(),nn(),Gt()}}),Jn={};async function Qn(e,t){const{data:r}=await e.from("metadata").select("domains, levels, function_tags").eq("project_id",t).maybeSingle();return{domains:r?.domains??[],levels:r?.levels??[],functionTags:Array.isArray(r?.function_tags)?r.function_tags.filter(e=>"string"==typeof e):[]}}async function Gn(e,t,r,i,n){const{error:a}=await e.from("metadata").upsert({project_id:t,domains:r,levels:i,...void 0!==n?{function_tags:n}:{}},{onConflict:"project_id"});if(a)throw new Error(a.message)}async function Yn(e){try{const t=await ze(),{domains:r}=await Qn(t,e.project_id),{counts:i,orphans:n}=await async function(e,t,r){const{data:i}=await e.from("items").select("data").eq("project_id",t).is("deleted_at",null),n={};for(const e of r)n[e]=0;const a={};for(const e of i??[]){const t=e.data?.tags?.domains??[];for(const e of t)a[e]=(a[e]??0)+1,e in n&&n[e]++}const s=new Set(r),o={};for(const[e,t]of Object.entries(a))s.has(e)||(o[e]=t);return{counts:n,orphans:o}}(t,e.project_id,r),a=r.map(e=>({name:e,registered:!0,item_count:i[e]??0})),s=Object.entries(n).map(([e,t])=>({name:e,registered:!1,item_count:t})).sort((e,t)=>e.name.localeCompare(t.name)),o=[...a,...s];return Bt(xt({domains:o,total:o.length,registered_count:a.length,unregistered_count:s.length,note:s.length>0?`${s.length} unregistered tag(s) found on items. Use atoms_create_domain to register them, or atoms_update_item to remove them.`:void 0}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Jt(Ot()):Jt(Lt(e instanceof Error?e.message:String(e)))}}async function Kn(e){try{const t=await ze();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Jt(At("Viewer"));throw e}const{domains:r,levels:i}=await Qn(t,e.project_id),n=e.name.trim().toLowerCase();return n?r.includes(n)?Jt(Rt(`Domain "${n}" already exists in this project.`)):(await Gn(t,e.project_id,[...r,n],i),Bt(xt({domain:{name:n},message:`Domain "${n}" registered. 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Bt(xt({deleted:!0,name:s,items_updated:l,message:l>0?`Domain "${s}" deleted and stripped from ${l} item${l>1?"s":""}.`:`Domain "${s}" deleted.`}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Jt(Ot()):Jt(Lt(e instanceof Error?e.message:String(e)))}}I(Jn,{createDomainHandler:()=>Kn,deleteDomainHandler:()=>Xn,listDomainsHandler:()=>Yn,updateDomainHandler:()=>Zn});var ea=E({"src/tools/domains.ts"(){Ne(),nn(),Gt(),vi()}}),ta={};async function ra(e){try{const t=await ze(),{data:r,error:i}=await t.from("projects").select("id, name").eq("id",e.project_id).is("deleted_at",null).maybeSingle(),n=r?.name??null,a=i?.message??null,{data:s,error:o}=await t.from("items").select("id, type, data").eq("project_id",e.project_id).is("deleted_at",null);if(o)throw new Error(o.message);const d=s??[];if(!n&&0===d.length){if(a)throw new Error(a);return Jt(It("Project",e.project_id))}const c={requirements:0,test_cases:0,notes:0},l=[],m=[];for(const e of d)if("requirement"===e.type){c.requirements++;const t=e.data?.tags?.domains??[];m.push({id:e.id,domains:t})}else"test-case"===e.type?(c.test_cases++,l.push(e.id)):"note"===e.type&&c.notes++;const p={passed:0,failed:0,blocked:0,not_run:0};if(l.length>0){const{data:r,error:i}=await t.from("test_results").select("item_id, result, run_at").eq("project_id",e.project_id).order("run_at",{ascending:!1});if(i)throw new Error(i.message);const n=new Map;for(const e of r??[])n.has(e.item_id)||n.set(e.item_id,e.result);for(const e of l){const t=n.get(e);t&&"not-run"!==t?"passed"===t?p.passed++:"failed"===t?p.failed++:"blocked"===t?p.blocked++:p.not_run++:p.not_run++}}const{data:u,error:_}=await t.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(_)throw new Error(_.message);const f=sr(s??[],u??[]),h=new Set;for(const e of f)"verifies"===e.type?h.add(e.to_id):"verified_by"===e.type&&h.add(e.from_id);const g=m.filter(e=>h.has(e.id)).length,y=m.length,w={covered:g,uncovered:y-g,total:y,percent:y>0?Math.round(g/y*1e3)/10:100},b=new Map;for(const e of m){const t=e.domains.length>0?e.domains:["(untagged)"],r=h.has(e.id);for(const e of t){b.has(e)||b.set(e,{covered:0,total:0});const t=b.get(e);t.total++,r&&t.covered++}}const v=Array.from(b.entries()).sort((e,t)=>e[0].localeCompare(t[0])).map(([e,t])=>({domain:e,covered:t.covered,total:t.total,percent:t.total>0?Math.round(t.covered/t.total*1e3)/10:100})),j=new Date;j.setDate(j.getDate()-7);const{count:S,error:x}=await t.from("change_history").select("id",{count:"exact",head:!0}).eq("project_id",e.project_id).gte("changed_at",j.toISOString());if(x)throw new Error(x.message);return Bt(xt({project_id:e.project_id,project_name:n??`Project ${e.project_id.slice(0,8)}`,counts:c,test_status:p,coverage:w,coverage_by_domain:v,recent_changes:S??0,last_updated:(new Date).toISOString()}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Jt(Ot()):Jt(Lt(e instanceof Error?e.message:String(e)))}}I(ta,{projectSummaryHandler:()=>ra});var ia,na=E({"src/tools/project-summary.ts"(){Ne(),dr(),Gt()}}),aa={};async function sa(e){try{const t=await ze();let r,i;if(e.query&&e.query.trim().length>0){const n=await ar(t,e.project_id,e.query,{type:e.type,limit:e.limit});r=n.items.map(e=>({id:e.id,title:e.title,type:e.type,status:e.data?.status,domains:e.data?.tags?.domains??[],level:e.data?.tags?.level})),i=n.totalCount}else{const n=await Xt(t,e.project_id,{type:e.type,domain:e.domain,level:e.level,limit:e.limit,offset:e.offset});r=n.items.map(e=>({id:e.id,title:e.title,type:e.type,status:e.data?.status,domains:e.data?.tags?.domains??[],level:e.data?.tags?.level})),i=n.totalCount}const n=await async function(e,t){const{data:r,error:i}=await e.from("items").select("data").eq("project_id",t).is("deleted_at",null);if(i)throw new Error(i.message);const n=new Set,a=new Set;for(const e of r??[]){const t=e.data?.tags;if(t){const e=t.domains;if(e)for(const t of e)n.add(t);const r=t.level;r&&a.add(r)}}return{domains:[...n].sort(),levels:[...a].sort()}}(t,e.project_id);return Bt(xt({items:r,filters:{domains:n.domains,levels:n.levels,types:ia},project_id:e.project_id},kt(i,e.limit,e.offset)))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Jt(Ot()):Jt(Lt(e instanceof Error?e.message:String(e)))}}I(aa,{browseHandler:()=>sa});var oa,da,ca,la,ma=E({"src/tools/browse.ts"(){Ne(),dr(),Gt(),ia=["requirement","test-case","note","table"]}}),pa={};async function ua(e){try{const t=e.direction??"downstream",r=null!=e.depth?Math.min(Math.max(e.depth,1),20):null,i=await ze(),n=await er(i,e.project_id,e.item_id);if(!n)return Jt(It("Item",e.item_id));const{data:a,error:s}=await i.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(s)throw new Error(s.message);const{data:o,error:d}=await i.from("items").select("id, title, type").eq("project_id",e.project_id).is("deleted_at",null);if(d)throw new Error(d.message);const c=new Map;for(const e of o??[])c.set(e.id,{title:e.title,type:e.type});const l=new Map,m=(e,t,r)=>{l.has(e)||l.set(e,[]),l.get(e).push({neighbor:t,relType:r})};for(const e of a??[]){const r=e.type;"upstream"!==t&&"both"!==t||(da.includes(r)&&m(e.from_id,e.to_id,r),ca.includes(r)&&m(e.to_id,e.from_id,la[r]??r)),"downstream"!==t&&"both"!==t||(ca.includes(r)&&m(e.from_id,e.to_id,r),da.includes(r)&&m(e.to_id,e.from_id,la[r]??r)),"related"===r&&(m(e.from_id,e.to_id,"related"),m(e.to_id,e.from_id,"related"))}const p=new Set;p.add(e.item_id);const u=[];let _=0;const f=[];for(const t of l.get(e.item_id)??[])f.push({id:t.neighbor,depth:1,path:[{from_id:e.item_id,to_id:t.neighbor,relationship_type:t.relType}]});for(;f.length>0&&u.length<oa;){const{id:e,depth:t,path:i}=f.shift();if(p.has(e))continue;if(null!==r&&t>r)continue;p.add(e);const n=c.get(e);if(n&&(u.push({item_id:e,title:n.title,type:n.type,depth:t,relationship_path:i}),t>_&&(_=t),null===r||t<r))for(const r of l.get(e)??[])p.has(r.neighbor)||f.push({id:r.neighbor,depth:t+1,path:[...i,{from_id:e,to_id:r.neighbor,relationship_type:r.relType}]})}let h=0;if(e.include_variable_refs){const{data:t}=await i.from("variable_references").select("variable_id").eq("item_id",e.item_id).eq("project_id",e.project_id),r=[...new Set((t??[]).map(e=>e.variable_id))];if(r.length>0){const{data:t}=await i.from("project_variables").select("id, name").in("id",r),n=new Map((t??[]).map(e=>[e.id,e.name])),{data:a}=await i.from("variable_references").select("variable_id, item_id").in("variable_id",r).eq("project_id",e.project_id).neq("item_id",e.item_id);for(const t of a??[]){const r=t.item_id;if(p.has(r))continue;if(u.length>=oa)break;p.add(r);const i=c.get(r);if(!i)continue;const a=n.get(t.variable_id)??t.variable_id;u.push({item_id:r,title:i.title,type:i.type,depth:1,relationship_path:[{from_id:e.item_id,to_id:r,relationship_type:`variable_ref:${a}`}]}),h++}}}const g={};for(const e of u)g[e.type]=(g[e.type]??0)+1;const y=c.get(e.item_id);return Bt(xt({root:{item_id:e.item_id,title:y?.title??n.title,type:y?.type??n.type},impacted_items:u,summary:{total_impacted:u.length,by_type:g,max_depth_reached:_,...h>0?{variable_impact_count:h}:{},...u.length>=oa?{truncated:!0}:{}}}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Jt(Ot()):Jt(Lt(e instanceof Error?e.message:String(e)))}}I(pa,{impactAnalysisHandler:()=>ua});var _a=E({"src/tools/impact-analysis.ts"(){Ne(),dr(),Gt(),oa=200,da=["parent","verifies","traces_to","allocated_from","decomposed_from"],ca=["child","verified_by","allocated_to","decomposes_to","traced_by"],la={parent:"child",child:"parent",verifies:"verified_by",verified_by:"verifies",related:"related",traces_to:"traced_by",traced_by:"traces_to",allocated_to:"allocated_from",allocated_from:"allocated_to",decomposes_to:"decomposed_from",decomposed_from:"decomposes_to"}}}),fa=E({"src/core/relationship-sync.ts"(){}}),ha={};function ga(e){return e instanceof Error&&e.message.includes("Not authenticated")?Jt(Ot()):null}async function ya(e,t){const{data:r,error:i}=await e.rpc("restore_baseline_state",{p_baseline_id:t.baselineId,p_project_id:t.projectId,p_items:[],p_variables:[],p_user_id:t.userId});if(i)throw new Error(i.message);return r}async function wa(e,t,r){const{data:i,error:n}=await e.from("items").select("id, deleted_at").eq("project_id",t).eq("id",r).maybeSingle();if(n)throw new Error(n.message);if(a=i,!Boolean(a?.id&&null===a.deleted_at))return;var a;const{error:s}=await e.rpc("sync_item_relationships_from_jsonb",{p_project_id:t,p_item_id:r});if(s)throw new Error(s.message)}async function ba(e,t,r){const{data:i,error:n}=await e.from("projects").select("org_id").eq("id",t).maybeSingle();if(n)return Jt(Lt(n.message));if(!i)return Jt(It("Project",t));const{data:a,error:s}=await e.from("organizations").select("feature_flags").eq("id",i.org_id).maybeSingle();return s?Jt(Lt(s.message)):!0!==(a?.feature_flags??{})[r]?Jt(Et(`Feature '${r}' is not enabled for this organization`,["Ask an org admin to enable the flag in Org Settings."])):null}async function va(e){try{const t=await ze(),r=await async function(e,t){const{data:r,error:i}=await e.from("baselines").select("id, project_id, name, description, field_definitions_snapshot, snapshot_at, created_at, created_by, locked_at, locked_by, release_version, release_status").eq("project_id",t).is("deleted_at",null).order("snapshot_at",{ascending:!1});if(i)throw new Error(`listBaselines: ${i.message}`);return r??[]}(t,e.project_id),i=Math.max(e.offset??0,0),n=Math.min(Math.max(e.limit??50,1),100);return Bt(xt({baselines:r.slice(i,i+n).map(e=>({id:e.id,name:e.name,description:e.description,field_definitions_snapshot:e.field_definitions_snapshot,snapshot_at:e.snapshot_at,created_at:e.created_at,created_by:e.created_by,locked:null!==e.locked_at,locked_at:e.locked_at,release_version:e.release_version,release_status:e.release_status})),total:r.length,offset:i,limit:n}))}catch(e){return ga(e)??Jt(Lt(e instanceof Error?e.message:String(e)))}}async function ja(e){try{const t=await ze(),r=await ba(t,e.project_id,"baselines_enabled");if(r)return r;const{data:i,error:n}=await t.from("baselines").insert({project_id:e.project_id,name:e.name.trim(),description:e.description??null,snapshot_at:(new Date).toISOString()}).select().single();return n?"23505"===n.code?Jt(Et(`Baseline name "${e.name}" already exists in this project`,["Pick a different name"])):Jt(Lt(n.message)):Bt(xt({id:i.id,name:i.name,description:i.description,field_definitions_snapshot:i.field_definitions_snapshot,snapshot_at:i.snapshot_at,created_at:i.created_at,locked:!1}))}catch(e){return ga(e)??Jt(Lt(e instanceof Error?e.message:String(e)))}}async function Sa(e){try{const t=await ze(),r=await rr(t,e.baseline_id);if(!r)return Jt(It("Baseline",e.baseline_id));const i=await ba(t,r.project_id,"baselines_enabled");if(i)return i;if(null!==r.locked_at)return Jt(Et("Baseline is already locked",["Locks are one-way; nothing to do"]));const{data:n}=await t.from("projects").select("org_id").eq("id",r.project_id).maybeSingle();if(!n)return Jt(It("Project",r.project_id));const{data:a}=await t.auth.getUser(),s=a?.user?.id;if(!s)return Jt(Ot());const{data:o}=await t.from("org_members").select("role").eq("user_id",s).eq("org_id",n.org_id).maybeSingle();if(!o||"admin"!==o.role)return Jt(Et("Only admins can lock baselines",["Ask an org admin to lock this baseline"]));const{data:d,error:c}=await t.from("baselines").update({locked_at:(new Date).toISOString(),locked_by:s}).eq("id",e.baseline_id).select().single();return c?Jt(Lt(c.message)):Bt(xt({id:d.id,locked_at:d.locked_at,locked_by:d.locked_by}))}catch(e){return ga(e)??Jt(Lt(e instanceof Error?e.message:String(e)))}}async function xa(e){try{const t=await ze(),[r,i]=await Promise.all([rr(t,e.baseline_a_id),rr(t,e.baseline_b_id)]);if(!r||!i)return Jt(It("Baseline","one of the baseline_ids"));if(r.project_id!==i.project_id)return Jt(Et("Both baselines must belong to the same project",["Verify both baseline_ids are from the same project_id"]));const[n,a]=await Promise.all([nr(t,r.project_id,r.snapshot_at),nr(t,i.project_id,i.snapshot_at)]),s=new Map(n.map(e=>[e.id,e])),o=new Map(a.map(e=>[e.id,e])),d=Array.from(new Set([...s.keys(),...o.keys()])).sort(),c=[];let l=0,m=0,p=0;for(const e of d){const t=s.get(e),r=o.get(e);if(!t&&r)l++,c.push({item_id:e,change_type:"added"});else if(t&&!r)m++,c.push({item_id:e,change_type:"removed"});else if(t&&r){const i=[];t.title!==r.title&&i.push("title"),t.type!==r.type&&i.push("type");JSON.stringify(t.data??{})!==JSON.stringify(r.data??{})&&i.push("data"),i.length>0&&(p++,c.push({item_id:e,change_type:"modified",fields_changed:i}))}}const u=Math.max(e.offset??0,0),_=Math.min(Math.max(e.limit??50,1),200),f=e.detail?c.slice(u,u+_):c.slice(u,u+_).map(({item_id:e,change_type:t,fields_changed:r})=>({item_id:e,change_type:t,fields_changed:r}));return Bt(xt({summary:{added:l,removed:m,modified:p,total_compared:d.length},items:f,page_info:{offset:u,limit:_,total:c.length},baselines:{a:{id:r.id,name:r.name,snapshot_at:r.snapshot_at},b:{id:i.id,name:i.name,snapshot_at:i.snapshot_at}}}))}catch(e){return ga(e)??Jt(Lt(e instanceof Error?e.message:String(e)))}}async function ka(e){try{const t=await ze(),r=await rr(t,e.baseline_id);if(!r)return Jt(It("Baseline",e.baseline_id));const i=await ba(t,r.project_id,"baselines_enabled");if(i)return i;const{data:n}=await t.from("projects").select("org_id").eq("id",r.project_id).maybeSingle();if(!n)return Jt(It("Project",r.project_id));const{data:a}=await t.auth.getUser(),s=a?.user?.id;if(!s)return Jt(Ot());const{data:o}=await t.from("org_members").select("role").eq("user_id",s).eq("org_id",n.org_id).maybeSingle();if(!o||"admin"!==o.role)return Jt(Et("Only admins can restore from a baseline",["Ask an org admin to run the restore"]));const{data:d}=await t.rpc("cc_project_is_controlled",{p_project_id:r.project_id});if(!0===d)return Jt(Et("Change control is on for this project. Release review before restoring a baseline.",["Release review on the project, then run the restore"]));const c=await nr(t,r.project_id,r.snapshot_at),l=c.map(e=>e.id),{data:m,error:p}=l.length>0?await t.from("items").select("*").eq("project_id",r.project_id).in("id",l):{data:[],error:null};if(p)return Jt(Lt(p.message));const u=function(e,t){const r=new Map(t.map(e=>[e.id,e]));return e.flatMap(e=>{const t=r.get(e.id),i=[];var n,a;return t?(null!==t.deleted_at&&i.push("deleted_at"),t.type!==e.type&&i.push("type"),t.title!==e.title&&i.push("title"),n=t.data,a=e.data,JSON.stringify(n??{})!==JSON.stringify(a??{})&&i.push("data")):i.push("missing"),0===i.length?[]:[{id:e.id,type:e.type,title:e.title,data:e.data??{},diff_summary:{changed_fields:i,restored:!0},oldData:t?.data??null}]})}(c,m??[]),{data:_,error:f}=await t.rpc("variables_at",{p_project_id:r.project_id,p_snapshot_at:r.snapshot_at});if(f)return Jt(Lt(f.message));const h=_??[];if(!0!==e.confirm)return Bt(xt({preview:!0,items_to_restore:u.length,variables_to_restore:h.length,field_definitions_to_restore:r.field_definitions_snapshot?.length??null}));const g=await ya(t,{baselineId:r.id,projectId:r.project_id,userId:s});return Bt(xt({ok:!0,items_restored:g.items_restored,variables_restored:g.variables_restored,field_definitions_restored:g.field_definitions.length}))}catch(e){return ga(e)??Jt(Lt(e instanceof Error?e.message:String(e)))}}I(ha,{createBaselineHandler:()=>ja,diffBaselinesHandler:()=>xa,listBaselinesHandler:()=>va,lockBaselineHandler:()=>Sa,restoreBaselineHandler:()=>ka,restoreBaselineStateAtomically:()=>ya,syncRestoredItemRelationships:()=>wa});var Ea,Ia=E({"src/tools/baselines.ts"(){Ne(),is(),Gt(),dr(),fa()}}),Aa={};function Ra(e){return"safety-goal"===e?"hara":"failure-mode"===e?"dfmea":null}async function Oa(e,t,r){const{data:i,error:n}=await e.rpc("next_item_id",{p_project_id:t,p_prefix:r});if(n)throw new Error(`ID generation failed: ${n.message}`);return i}function za(e){const t=e?.relationships?.mitigated_by;return Array.isArray(t)?t.filter(e=>"string"==typeof e):[]}function Da(e){return JSON.parse(JSON.stringify(e??{}))}async function Ha(e,t,r){const i=[];for(const e of r){const t=(e??"").trim();t&&null===li(t,i)&&i.push(t)}if(0===i.length)return i;try{const{data:r}=await e.from("metadata").select("domains, function_tags").eq("project_id",t).maybeSingle(),n=e=>Array.isArray(e)?e.filter(e=>"string"==typeof e):[],a=n(r?.domains),s=n(r?.function_tags),o=i.map(e=>li(e,a)??e),d=[...a],c=[...s];let l=!1;for(const e of o)null===li(e,d)&&(d.push(e),l=!0),null===li(e,c)&&(c.push(e),l=!0);if(l){const{error:r}=await e.from("metadata").upsert({project_id:t,domains:d,function_tags:c},{onConflict:"project_id"});r&&process.stderr.write(`[atoms-mcp] Warning: function tag registration failed: ${r.message}\n`)}return o}catch(e){return process.stderr.write(`[atoms-mcp] Warning: function tag registration failed: ${e instanceof Error?e.message:String(e)}\n`),i}}async function Ua(e){try{const t=await ze(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Jt(At("Viewer"));throw e}const i=e.source_req_ids??[],n=e.source_functions??[];if("hara"===e.subtype&&i.length>0)return Jt(Rt("A HARA is seeded from functions, never requirements (a requirement is an output of the analysis): pass source_functions and omit source_req_ids"));if("dfmea"===e.subtype&&n.length>0)return Jt(Rt("source_functions applies to hara only; seed a DFMEA with source_req_ids"));if(i.length>50)return Jt(Rt("source_req_ids supports at most 50 entries per call"));if(n.length>50)return Jt(Rt("source_functions supports at most 50 entries per call"));if(i.length>0){const{data:r,error:n}=await t.from("items").select("id, type, data").eq("project_id",e.project_id).is("deleted_at",null).in("id",i);if(n)throw new Error(n.message);const a=new Map((r??[]).map(e=>[e.id,e])),s=i.filter(e=>!a.has(e));if(s.length>0)return Jt(It("Source requirement(s)",s.join(", ")));const o=i.filter(e=>{const t=a.get(e);return"requirement"!==t.type||Ea.has(t.data?.req_type)});if(o.length>0)return Jt(Rt(`source_req_ids must reference plain requirements (type='requirement', not analysis rows): ${o.join(", ")}`))}const a=e.subtype,s="hara"===a?await Ha(t,e.project_id,n):i,o=await Oa(t,e.project_id,ai[a]),d=e.title??("hara"===a?"New HARA":"New DFMEA"),c=e.revision??"1.0",l=ii[a],m=(new Date).toISOString(),p={id:o,type:"analysis",title:d,body:"",tags:{domains:[],level:""},ownership:{primary:null,additional:[]},relationships:{parents:[],children:[],related:[],verifies:[],verified_by:[]},links:[],analysis:{subtype:a,scheme:si[a],revision:c,..."hara"===a?{standard:oi}:{}},metadata:{created_at:m,created_by:r,updated_at:m,updated_by:r}},{error:u}=await t.rpc("save_item_with_revision",{p_item_id:o,p_project_id:e.project_id,p_type:"analysis",p_title:d,p_data:p,p_user_id:r,p_event_source:"mcp",p_event_session_id:es()??null,p_diff_summary:null});if(u)throw new Error(u.message);const _=(e,t)=>"hara"===a?{id:e,source_function:t}:{id:e,source_req:t},f=[],h=[];for(const i of s){const n=await Oa(t,e.project_id,ni[a]),s={id:n,type:"requirement",title:"",body:"",req_type:l,tags:{domains:[],level:""},ownership:{primary:null,additional:[]},relationships:{parents:[o],children:[],related:[],verifies:[],verified_by:[]},links:[],analysis_props:"hara"===a?{source_req:null,source_function:i,approved:!1,approved_at:null,field_source:{}}:{source_req:i,approved:!1,approved_at:null,field_source:{}},metadata:{created_at:m,created_by:r,updated_at:m,updated_by:r}},{error:d}=await t.rpc("save_item_with_revision",{p_item_id:n,p_project_id:e.project_id,p_type:"requirement",p_title:"",p_data:s,p_user_id:r,p_event_source:"mcp",p_event_session_id:es()??null,p_diff_summary:null});if(d)throw new Error(d.message);const{error:c}=await t.rpc("apply_link_change",{p_project_id:e.project_id,p_from_id:n,p_to_id:o,p_type:"parent",p_action:"add",p_user_id:r,p_event_source:"mcp"});c&&(process.stderr.write(`[atoms-mcp] Warning: analysis row parent link sync failed for ${n}: ${c.message}\n`),h.push({row_id:n,..."hara"===a?{source_function:i}:{source_req:i},message:c.message})),await t.from("change_history").insert({item_id:n,project_id:e.project_id,changed_by:r,event_type:"created",old_data:null,new_data:s,actor:ts(),session_id:es()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),f.push(_(n,i))}return await t.from("change_history").insert({item_id:o,project_id:e.project_id,changed_by:r,event_type:"created",old_data:null,new_data:p,actor:ts(),session_id:es()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),Bt(xt({id:o,subtype:a,title:d,revision:c,..."hara"===a?{standard:oi}:{},rows:f,...h.length>0?{link_warnings:h,warning:`${h.length} row(s) were created but could not be attached to the analysis and will not appear in atoms_get_analysis. Repair: for each row in link_warnings, call atoms_link_items with type 'parent', from_id=<row id>, to_id=${o}.`}:{}}))}catch(e){return Jt($t(e))}}async function Ca(e){try{const t=await ze(),r=Ce();try{await Te(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Jt(At("Viewer"));throw e}const i=await er(t,e.project_id,e.row_id);if(!i)return Jt(It("Analysis row",e.row_id));const n=i.data,a=Ra(n?.req_type);if(!a)return Jt(Rt(`Item ${e.row_id} is not an analysis row (req_type must be 'safety-goal' or 'failure-mode')`));const s=new Set([...ri[a],"effect"]);"hara"===a&&s.add("title");const o=Object.keys(e.fields??{});if(0===o.length)return Jt(Rt("fields must contain at least one key"));const d=o.filter(e=>!s.has(e));if(d.length>0)return Jt(Rt(`Unknown field(s) for ${a}: ${d.join(", ")}. Allowed: ${[...s].sort().join(", ")}`));const c=ti[a],l={};for(const t of o){const r=e.fields[t];if(c[t]){const e="number"==typeof r&&"dfmea"===a?String(r):r;if("string"!=typeof e||!c[t].includes(e))return Jt(Rt(`Invalid ${t} value ${JSON.stringify(r)} for ${a}. Allowed: ${c[t].join(", ")}`));l[t]=e}else{if("string"!=typeof r)return Jt(Rt(`Field '${t}' must be a string`));l[t]=r}}if("hara"===a&&"string"==typeof l.source_function&&l.source_function.trim()){const[r]=await Ha(t,e.project_id,[l.source_function]);r&&(l.source_function=r)}const m=n?.analysis_props??null,p=Da(n);p.analysis_props&&"object"==typeof p.analysis_props||(p.analysis_props={source_req:null,approved:!1,approved_at:null,field_source:{}});const u=p.analysis_props;u.field_source&&"object"==typeof u.field_source||(u.field_source={});let _=i.title;for(const[e,t]of Object.entries(l))"effect"===e?p.body=t:"title"===e?(p.title=t,_=t):(u[e]=t,"failure_mode"===e&&"dfmea"===a&&(p.title=t,_=t)),u.field_source[e]="mcp";const f=(new Date).toISOString();p.metadata={...p.metadata??{},updated_at:f,updated_by:r};const{data:h,error:g}=await t.rpc("save_item_with_revision",{p_item_id:i.id,p_project_id:e.project_id,p_type:i.type,p_title:_,p_data:p,p_user_id:r,p_event_source:"mcp",p_event_session_id:es()??null,p_diff_summary:null,p_expected_updated_at:i.updated_at});if(g)throw new Error(g.message);if(!h)return Jt(Et(`Fill silently failed for '${e.row_id}': save RPC returned no row. Likely RLS denied the write.`,["Verify you have editor or admin role in this project","Retry after checking project access"]));await t.from("change_history").insert({item_id:i.id,project_id:e.project_id,changed_by:r,event_type:"updated",old_data:n,new_data:p,actor:ts(),session_id:es()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)});const y=ui(a,u),w=[];if("hara"===a){const n=ui("hara",m),a=za(p);if(a.length>0&&y!==Kr&&y!==n)for(const n of a){const a=await er(t,e.project_id,n);if(!a)continue;const s=a.data;if(s?.asil===y&&s?.asil_source===i.id)continue;const o=s?.asil??null,d=s?.asil_source??null,c=Da(s);c.asil=y,c.asil_source=i.id,c.metadata={...c.metadata??{},updated_at:f,updated_by:r};const{error:l}=await t.rpc("save_item_with_revision",{p_item_id:a.id,p_project_id:e.project_id,p_type:a.type,p_title:a.title,p_data:c,p_user_id:r,p_event_source:"mcp",p_event_session_id:es()??null,p_diff_summary:null,p_expected_updated_at:a.updated_at});if(l)throw new Error(l.message);await t.from("change_history").insert({item_id:a.id,project_id:e.project_id,changed_by:r,event_type:"updated",old_data:{asil:o,asil_source:d},new_data:{asil:y,asil_source:i.id},actor:ts(),session_id:es(),reason:`ASIL propagated from ${i.id} (rating change via atoms_fill_row)`}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),w.push(n)}}return Bt(xt({row_id:i.id,subtype:a,written_fields:Object.keys(l),computed_level:y,...w.length>0?{asil_propagated_to:w}:{}}))}catch(e){return Jt($t(e))}}async function qa(e,t,r){const i=await er(e,t,r);if(!i)return{ok:!1,result:Jt(It("Analysis",r))};if("analysis"!==i.type)return{ok:!1,result:Jt(Rt(`Item ${r} is not an analysis (type='${i.type}')`))};const n=i.data,a=Ra("hara"===n?.analysis?.subtype?"safety-goal":"dfmea"===n?.analysis?.subtype?"failure-mode":null);if(!a)return{ok:!1,result:Jt(Rt(`Analysis ${r} is missing a valid analysis.subtype`))};const s=ii[a],o=Array.isArray(n?.relationships?.children)?n.relationships.children.filter(e=>"string"==typeof e):[];let d=[];if(o.length>0){const{data:r,error:i}=await e.from("items").select("*").eq("project_id",t).is("deleted_at",null).in("id",o);if(i)throw new Error(i.message);const n=new Map((r??[]).filter(e=>!e.deleted_at&&o.includes(e.id)&&e.data?.req_type===s).map(e=>[e.id,e]));d=o.map(e=>n.get(e)).filter(e=>Boolean(e))}const c=new Set;for(const e of d){const t=e.data?.analysis_props??{};"string"==typeof t.source_req&&t.source_req&&c.add(t.source_req);for(const t of za(e.data))c.add(t)}const l=new Map;if(c.size>0){const{data:r,error:i}=await e.from("items").select("id, updated_at").eq("project_id",t).is("deleted_at",null).in("id",[...c]);if(i)throw new Error(i.message);for(const e of r??[])l.set(e.id,e.updated_at)}const m=d.map(e=>{const t=e.data?.analysis_props??{},r=za(e.data).filter(e=>l.has(e)),i=r.length>0,n=ui(a,t),s=function(e,t,r){if(r)return null;if("hara"===e){const e=mi(t);return"QM"!==e&&e!==Kr?`asil ${e} unmitigated`:null}const i=parseInt(pi(t),10),n=parseInt(t?.severity||"",10);return!Number.isNaN(i)&&i>=100?"rpn >= 100":!Number.isNaN(n)&&n>=9?"severity >= 9":null}(a,t,i),o={id:e.id,title:"string"==typeof e.title?e.title:"",source_req:"string"==typeof t.source_req?t.source_req:null,effect:"string"==typeof e.data?.body?e.data.body:"",computed_level:n,is_gap:null!==s,gap_rule:s,is_critical:_i(a,t,i),is_stale:fi(t,r,e=>l.get(e)??null),mitigated_by:r,link_roles:t.link_roles??{},approved:!0===t.approved,approved_at:t.approved_at??null,mcp_fields:Object.entries(t.field_source??{}).filter(([,e])=>"mcp"===e).map(([e])=>e).sort()};for(const e of ri[a])o[e]=t[e]??null;return o});return{ok:!0,analysis:{id:i.id,title:"string"==typeof i.title?i.title:"",subtype:a,scheme:"string"==typeof n?.analysis?.scheme?n.analysis.scheme:si[a],revision:"string"==typeof n?.analysis?.revision?n.analysis.revision:"1.0",standard:"string"==typeof n?.analysis?.standard?n.analysis.standard:"hara"===a?oi:null},rows:m,counts:{rows:m.length,gaps:m.filter(e=>e.is_gap).length,critical:m.filter(e=>e.is_critical).length,stale:m.filter(e=>e.is_stale).length,approved:m.filter(e=>e.approved).length,linked:m.filter(e=>e.mitigated_by.length>0).length}}}async function Ta(e){try{const t=await ze(),r=await qa(t,e.project_id,e.analysis_id);return r.ok?Bt(xt({analysis:r.analysis,rows:r.rows,counts:r.counts})):r.result}catch(e){return Jt($t(e))}}async function Ma(e){try{const n=await ze(),a=Ce();try{await Te(n,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Jt(At("Viewer"));throw e}if(e.row_id===e.req_id)return Jt(Rt("row_id and req_id must be different items"));const s=await er(n,e.project_id,e.row_id);if(!s)return Jt(It("Analysis row",e.row_id));const o=s.data,d=Ra(o?.req_type);if(!d)return Jt(Rt(`Item ${e.row_id} is not an analysis row (req_type must be 'safety-goal' or 'failure-mode')`));const c=await er(n,e.project_id,e.req_id);if(!c)return Jt(It("Requirement",e.req_id));const l=c.data;if("requirement"!==c.type||Ea.has(l?.req_type))return Jt(Rt(`req_id must reference a plain requirement (type='requirement', not an analysis row): ${e.req_id}`));if("dfmea"===d&&!e.role)return Jt(Rt(`role is required for dfmea mitigation links. Choose one of: ${Zr.join(", ")}`));if("hara"===d&&e.role)return Jt(Rt("role is not applicable to hara mitigation links; omit it (roles are a dfmea concept)"));let m=Kr;if("hara"===d){m=ui("hara",o?.analysis_props);const n=l?.asil;if(m!==Kr&&"string"==typeof n&&n.length>0&&n!==m&&!0!==e.override)return Jt((r=m,{...Et(`ASIL conflict: the target requirement already carries asil '${t=n}' but ${i=s.id} computes '${r}'.`,["Pass override=true to apply the HARA value; the override is history-logged like a dialog accept","Or align the row's S/E/C ratings with the existing ASIL before linking"]),details:{code:"asil_conflict",current_value:t,incoming_value:r,source_row:i,hint:"pass override=true to apply the HARA value; the override is history-logged like a dialog accept"}}))}const p="dfmea"===d?e.role:null,{error:u}=await n.rpc("apply_link_change",{p_project_id:e.project_id,p_from_id:e.row_id,p_to_id:e.req_id,p_type:"mitigated_by",p_action:"add",p_user_id:a,p_event_source:"mcp",p_expected_from_updated_at:s.updated_at,p_expected_to_updated_at:c.updated_at,p_role:p});if(u)throw new Error(u.message);let _;if(await n.from("change_history").insert({item_id:e.row_id,project_id:e.project_id,changed_by:a,event_type:"updated",old_data:null,new_data:{relationship_change:{action:"add",type:"mitigated_by",from:e.row_id,to:e.req_id,...p?{role:p}:{}}},actor:ts(),session_id:es()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),"hara"===d&&m!==Kr){const t=await er(n,e.project_id,e.req_id);if(t){const r=t.data,i=r?.asil??null,o=r?.asil_source??null,d=Da(r);d.asil=m,d.asil_source=s.id;const c=(new Date).toISOString();d.metadata={...d.metadata??{},updated_at:c,updated_by:a};const{error:l}=await n.rpc("save_item_with_revision",{p_item_id:t.id,p_project_id:e.project_id,p_type:t.type,p_title:t.title,p_data:d,p_user_id:a,p_event_source:"mcp",p_event_session_id:es()??null,p_diff_summary:null,p_expected_updated_at:t.updated_at});if(l)throw new Error(l.message);await n.from("change_history").insert({item_id:t.id,project_id:e.project_id,changed_by:a,event_type:"updated",old_data:{asil:i,asil_source:o},new_data:{asil:m,asil_source:s.id},actor:ts(),session_id:es(),reason:!0===e.override?`ASIL override accepted via atoms_link_mitigation (was '${i??"unset"}', now '${m}' from ${s.id})`:`ASIL set via atoms_link_mitigation from ${s.id}`}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),_=m}}return Bt(xt({row_id:e.row_id,req_id:e.req_id,type:"mitigated_by",role:p,..._?{asil_written:_}:{}}))}catch(e){return Jt($t(e))}var t,r,i}async function Pa(e){try{const t=await ze(),r=await qa(t,e.project_id,e.analysis_id);if(!r.ok)return r.result;const i=r.rows.filter(e=>e.is_gap).map(e=>({id:e.id,title:e.title,source_req:e.source_req,source_function:"string"==typeof e.source_function?e.source_function:null,computed_level:e.computed_level,rule:e.gap_rule}));return Bt(xt({analysis_id:r.analysis.id,subtype:r.analysis.subtype,gaps:i,count:i.length}))}catch(e){return Jt($t(e))}}I(Aa,{createAnalysisHandler:()=>Ua,fillRowHandler:()=>Ca,getAnalysisHandler:()=>Ta,getGapsHandler:()=>Pa,linkMitigationHandler:()=>Ma});var $a,Na,La,Fa,Wa,Va,Ba,Ja,Qa,Ga,Ya=E({"src/tools/analysis.ts"(){Ne(),dr(),is(),Gt(),vi(),Ea=new Set(["safety-goal","failure-mode"])}}),Ka={};function Za(e){F(e.toolName)&&function(e,t){const r=`ui://${t.toolName}/${t.htmlFile}`,i=function(e,t){const r=s.fileURLToPath("undefined"==typeof document?require("url").pathToFileURL(__filename).href:p&&"SCRIPT"===p.tagName.toUpperCase()&&p.src||new URL("index.cjs",document.baseURI).href),i=j.default.dirname(r);return j.default.resolve(i,"apps","src","apps",e,t)}(t.appName,t.htmlFile),n=[...Qt.resourceDomains,...t.extraResourceDomains??[]];d.registerAppTool(e,t.toolName,{title:t.title,description:t.description,inputSchema:t.inputSchema,annotations:t.annotations,_meta:{ui:{resourceUri:r}}},t.handler),d.registerAppResource(e,`${t.title} UI`,r,{mimeType:d.RESOURCE_MIME_TYPE},async()=>{const e=await v.default.readFile(i,"utf-8");return{contents:[{uri:r,mimeType:d.RESOURCE_MIME_TYPE,text:e,_meta:{ui:{csp:{resourceDomains:n}}}}]}})}(Fa,e)}function Xa(e,t){return async r=>{const i=O(P(),e);if(!i.allowed)return Jt(Et(`Tool ${e} is blocked by org policy.`,[D(i.reason),"Contact your org admin to adjust the MCP access policy."]));try{!function(e){const t=st();if(!t)return;if("object"!=typeof e||null===e)return;const r=e.project_id;if("string"==typeof r&&r!==t)throw new it(t,r)}(r)}catch(e){if(e instanceof it)return Jt(Dt(e.expectedProjectId));throw e}{const e=P(),t=r?.project_id;if(null!==e.project_scope&&"string"==typeof t&&!e.project_scope.includes(t))return Jt(Et("Tool call rejected: project_id is outside your org's MCP project scope.",[`Allowed projects: ${e.project_scope.length} project${1===e.project_scope.length?"":"s"} configured by your admin`,"Use atoms_list_projects to see which projects you can access in this session"]))}let n,a;try{a=await ze(),n=Ce()}catch{return t(r)}const s=await async function(e,t){const r=parseInt(process.env.ATOMS_RATE_LIMIT_RPM??"",10)||Xe,i=new Date,n=new Date(i.getTime()-et);try{const{count:a,error:s}=await t.from("mcp_rate_limits").select("id",{count:"exact",head:!0}).eq("user_id",e).gte("requested_at",n.toISOString());if(s)throw new Error(s.message);if((a??0)>=r){const{data:r,error:a}=await t.from("mcp_rate_limits").select("requested_at").eq("user_id",e).gte("requested_at",n.toISOString()).order("requested_at",{ascending:!0}).limit(1).maybeSingle();if(a)throw new Error(a.message);const s=(r?new Date(r.requested_at).getTime():i.getTime())+et-i.getTime();return{allowed:!1,retryAfterSeconds:Math.max(1,Math.ceil(s/1e3))}}t.from("mcp_rate_limits").insert({user_id:e,requested_at:i.toISOString()}).then(({error:e})=>{e&&process.stderr.write(`[rate-limiter] insert failed: ${e.message}\n`)});const o=new Date(i.getTime()-2*et);return t.from("mcp_rate_limits").delete().eq("user_id",e).lt("requested_at",o.toISOString()).then(()=>{}),{allowed:!0}}catch(e){return process.stderr.write(`[rate-limiter] DB check failed (${e instanceof Error?e.message:String(e)}), falling back to allow.\n`),{allowed:!0}}}(n,a);if(!s.allowed)return Jt(Ht(s.retryAfterSeconds));if("1"===process.env.ATOMS_MCP_LOCKDOWN||"true"===process.env.ATOMS_MCP_LOCKDOWN){const e=r?.project_id;if("string"==typeof e)try{const{requireWriteAccess:t}=await Promise.resolve().then(()=>(Ne(),Oe));await t(a,e)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message){const{accessDeniedError:e}=await Promise.resolve().then(()=>(Gt(),vt));return Jt(e("Viewer (lockdown mode: read access requires editor or admin)"))}}}const o=function(){const e=performance.now();return()=>Math.round(performance.now()-e)}();let d,c="success";try{const e=await t(r),i=e;if(!0===i?.isError){c="error";const e=i?.content;if(e?.[0]?.text)try{d=JSON.parse(e[0].text).message}catch{}}return e}catch(e){throw c="error",d=e instanceof Error?e.message:String(e),e}finally{const t={tool_name:e,params:r,status:c,duration_ms:o(),error_msg:d,project_id:r.project_id,session_id:Va,client_name:Ba};try{!function(e,t,r){const i=Ze(r.params);e.from("mcp_audit_log").insert({user_id:t,tool_name:r.tool_name,params:i,status:r.status,duration_ms:r.duration_ms,error_msg:r.error_msg??null,project_id:r.project_id??null,session_id:r.session_id??null,client_name:r.client_name??null}).then(({error:e})=>{e&&process.stderr.write(`[audit] Failed to log: ${e.message}\n`)})}(await ze(),n,t)}catch{}}}}function es(){return Va}function ts(){return Ja}function rs(){return Ba}I(Ka,{ATOMS_MCP_SERVER_VERSION:()=>La,getMcpActor:()=>ts,getMcpClientName:()=>rs,getMcpSessionId:()=>es,server:()=>Fa});var is=E({"src/server.ts"(){nt(),at(),B(),dt(),$(),T(),yt(),wt(),Ne(),Gt(),Yt(),$a=l.createRequire("undefined"==typeof document?require("url").pathToFileURL(__filename).href:p&&"SCRIPT"===p.tagName.toUpperCase()&&p.src||new URL("index.cjs",document.baseURI).href),Na=$a("../package.json"),La=Na.version,Fa=new c.McpServer({name:"atoms-mcp-server",version:La}),Wa=(e,t,r)=>{if(F(e))return Fa.registerTool(e,t,r)},Va=a.randomUUID(),Ba=ct(process.env.ATOMS_CLIENT_NAME),Ja=function(){const e=ct(Ba);return"cursor"===e?"mcp_cursor":"copilot"===e?"mcp_copilot":"mcp_claude"}(),Wa("atoms_status",{title:"ATOMS MCP Health Check",description:'Check the health and authentication status of the ATOMS MCP server.\n\nCall this FIRST if other atoms tools fail or return auth errors.\nThis tool works WITHOUT authentication — it checks whether credentials\nexist and are valid, and tells the user exactly what to do if not.\n\nArgs: None\n\nReturns:\n { status: "authenticated"|"not_authenticated"|"expired", email, message, next_steps }\n\nExamples:\n - "Is ATOMS MCP working?" → atoms_status()\n - "Why are atoms tools failing?" → atoms_status()',inputSchema:{},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},async()=>{try{const{readCredentials:e,isTokenValid:t}=await Promise.resolve().then(()=>(oe(),J)),r=await e();if(!r)return{content:[{type:"text",text:JSON.stringify({status:"not_authenticated",message:"No ATOMS credentials found. You need to login first.",next_steps:["1. Open a terminal on your machine","2. Run: npx @atoms-tech/atoms-mcp login","3. Complete the login in your browser","4. Restart Claude Desktop (quit and reopen)","5. Try your query again"]},null,2)}]};if(!t(r))try{const{getValidToken:e}=await Promise.resolve().then(()=>(Re(),be)),{email:t}=await e(),{invalidateClient:r}=await Promise.resolve().then(()=>(Ne(),Oe));return r(),{content:[{type:"text",text:JSON.stringify({status:"authenticated",email:t,message:"Token was expired but has been refreshed. You're good to go!"},null,2)}]}}catch{return{content:[{type:"text",text:JSON.stringify({status:"expired",email:r.user_email??"unknown",message:"Your session has expired and could not be refreshed.",next_steps:["1. Open a terminal on your machine","2. Run: npx @atoms-tech/atoms-mcp logout","3. Run: npx @atoms-tech/atoms-mcp login","4. Complete the login in your browser","5. Restart Claude Desktop (quit and reopen)"]},null,2)}]}}return{content:[{type:"text",text:JSON.stringify({status:"authenticated",email:r.user_email??"unknown",message:"ATOMS MCP is connected and authenticated. All tools are ready."},null,2)}]}}catch(e){return{content:[{type:"text",text:JSON.stringify({status:"error",message:`Health check failed: ${e instanceof Error?e.message:String(e)}`,next_steps:["1. Open a terminal","2. Run: npx @atoms-tech/atoms-mcp login","3. Restart Claude Desktop"]},null,2)}]}}}),Wa("atoms_list_projects",{title:"List ATOMS Projects",description:'List all projects the authenticated user has access to.\n\nThis is the ENTRY POINT tool. Call this first to discover project IDs,\nthen use those IDs with all other tools.\n\nArgs: None\n\nReturns:\n { status: "success", data: [{ id, name, description, org_id, created_at }] }\n\nExamples:\n - "What projects do I have?" → atoms_list_projects()\n - "Show my projects" → atoms_list_projects()\n\nWorkflow:\n atoms_list_projects → atoms_list_items(project_id) → atoms_get_item(project_id, item_id)',inputSchema:{},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_list_projects",async()=>{const{listProjectsHandler:e}=await Promise.resolve().then(()=>(mr(),cr));return e()})),Wa("atoms_list_items",{title:"List ATOMS Items",description:'List items in an ATOMS project with optional type/domain/level filters.\n\nThis is the primary ENTRY POINT for discovering items. Use it to browse\nproject contents before drilling into specific items with atoms_get_item.\n\nArgs:\n - project_id (string, UUID): The project to list items from\n - type (string, optional): Filter: requirement|test-case|note|table\n - domain (string, optional): Filter by domain tag\n - level (string, optional): Filter by level (System, Subsystem, Component)\n - limit (number, optional): Max results, 1-200 (default 50)\n - offset (number, optional): Pagination offset (default 0)\n\nReturns:\n { status: "success", data: [{ id, title, type, status, domains, level }], meta: { total_count, limit, offset, has_more } }\n\nExamples:\n - "Show me all requirements" → atoms_list_items(project_id, type="requirement")\n - "What test cases exist?" → atoms_list_items(project_id, type="test-case")\n\nErrors:\n - "Project not found" → verify project_id\n - "Access denied" → check org membership',inputSchema:{project_id:o.z.string().uuid("Must be a valid project UUID").describe("UUID of the project"),type:o.z.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),domain:o.z.string().max(64).optional().describe("Filter by domain tag (e.g., 'Safety', 'Performance')"),level:o.z.string().max(32).optional().describe("Filter by level (System, Subsystem, Component)"),limit:o.z.number().int().min(1).max(200).default(50).describe("Max results (default 50, max 200)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset (default 0)"),baseline_id:o.z.string().uuid().optional().describe("Optional baseline UUID. Returns items as they were at that baseline's moment. Mutually exclusive with as_of."),as_of:o.z.string().datetime().optional().describe("Optional ISO 8601 timestamp. Returns items as they were at that moment. Mutually exclusive with baseline_id.")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_list_items",async e=>{const{listItemsHandler:t}=await Promise.resolve().then(()=>(fr(),pr));return t(e)})),Wa("atoms_get_item",{title:"Get ATOMS Item Details",description:'Get full details of a single item including relationships, test history, and ownership.\n\nUse after atoms_list_items or atoms_search to drill into a specific item.\n\nArgs:\n - project_id (string, UUID): The project containing the item\n - item_id (string): Item ID (e.g., "REQ-001", "TC-050")\n\nReturns:\n Full WorkItem with relationships, test runs, ownership, metadata.\n\nExamples:\n - "Show me requirement REQ-001" → atoms_get_item(project_id, "REQ-001")\n - "Get test case details" → atoms_get_item(project_id, "TC-050")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID (e.g., REQ-001)"),baseline_id:o.z.string().uuid().optional().describe("Optional baseline UUID. Returns the item as it was at that baseline's moment. Mutually exclusive with as_of."),as_of:o.z.string().datetime().optional().describe("Optional ISO 8601 timestamp. Returns the item as it was at that moment. Mutually exclusive with baseline_id.")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_get_item",async e=>{const{getItemHandler:t}=await Promise.resolve().then(()=>(wr(),hr));return t(e)})),Wa("atoms_search",{title:"Search ATOMS Items",description:'Full-text search across items in a project. Searches title, body, and summary.\n\nAlternative entry point to atoms_list_items when you know what you\'re looking for.\n\nArgs:\n - project_id (string, UUID): The project to search in\n - query (string): Search text (max 1000 chars)\n - type (string, optional): Filter by type\n - asset (string, optional): Filter to items with at least one run on the given asset\n (VIN, module, lot, ...). Case-sensitive exact match.\n - limit (number, optional): Max results, 1-100 (default 25)\n\nReturns:\n Matching items with @basic fields, ranked by relevance.\n\nExamples:\n - "Find braking requirements" → atoms_search(project_id, "braking system")\n - "Search for safety tests" → atoms_search(project_id, "safety", type="test-case")\n - "Tests that ran on this VIN" → atoms_search(project_id, "", asset="WEV...0005")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),query:o.z.string().min(1).max(1e3).describe("Search text"),type:o.z.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),asset:o.z.string().max(200).optional().describe("Filter to items with at least one run on this asset (case-sensitive exact)"),limit:o.z.number().int().min(1).max(100).default(25).describe("Max results (default 25, max 100)"),baseline_id:o.z.string().uuid().optional().describe("Optional baseline UUID. Searches within the project state at that baseline's moment.")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_search",async e=>{const{searchHandler:t}=await Promise.resolve().then(()=>(jr(),br));return t(e)})),Wa("atoms_semantic_search",{title:"Semantic Search ATOMS Items",description:'Meaning-based search across items using pgvector embeddings (GTE-small, 384d).\n\nUse when atoms_search (exact/substring) misses conceptually related items.\nBest for natural-language concept queries; atoms_search is better for exact phrases or IDs.\n\nArgs:\n - project_id (string, UUID): The project to search in\n - query (string): Natural-language concept query (max 1000 chars)\n - type (string, optional): Filter by type\n - limit (number, optional): Max results, 1-50 (default 10)\n\nReturns:\n Semantically similar items ranked by cosine similarity.\n\nExamples:\n - "Find braking-related requirements" → atoms_semantic_search(project_id, "braking deceleration stopping distance")\n - "Safety-related test cases" → atoms_semantic_search(project_id, "hazard risk mitigation safety", type="test-case")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),query:o.z.string().min(1).max(1e3).describe("Natural-language concept query"),type:o.z.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),limit:o.z.number().int().min(1).max(50).default(10).describe("Max results (default 10, max 50)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_semantic_search",async e=>{const{semanticSearchHandler:t}=await Promise.resolve().then(()=>(kr(),Sr));return t(e)})),Za({appName:"coverage",htmlFile:"coverage-app.html",toolName:"atoms_get_coverage",title:"Get Test Coverage Report",description:'Find requirements without linked test cases (coverage gaps).\n\nEssential for compliance reporting in safety-critical industries.\n\nIn MCP App hosts (Claude, ChatGPT), renders a visual coverage heatmap.\nFalls back to JSON for non-UI clients.\n\nArgs:\n - project_id (string, UUID): The project to analyze\n - domain (string, optional): Filter by domain\n - level (string, optional): Filter by level\n - baseline_id (string, UUID, optional): coverage at that baseline\'s moment\n - as_of (string ISO 8601, optional): coverage at that moment\n baseline_id and as_of are mutually exclusive.\n\nReturns:\n { covered, uncovered, total, coverage_percent, uncovered_items: [...] }\n\nExamples:\n - "What\'s our test coverage?" → atoms_get_coverage(project_id)\n - "Safety coverage gaps?" → atoms_get_coverage(project_id, domain="Safety")\n - "Coverage at PDR submission" → atoms_get_coverage(project_id, baseline_id="...")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),domain:o.z.string().max(64).optional().describe("Filter by domain tag"),level:o.z.string().max(32).optional().describe("Filter by level"),baseline_id:o.z.string().uuid().optional().describe("Compute coverage as of this baseline's snapshot moment"),as_of:o.z.string().datetime().optional().describe("Compute coverage as of this ISO 8601 moment")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Xa("atoms_get_coverage",async e=>{const{getCoverageHandler:t}=await Promise.resolve().then(()=>(Rr(),Er));return t(e)})}),Wa("atoms_verification_status",{title:"Get Release Verification Status",description:'Release-bound verification state per requirement, matching the in-app projection.\n\nEach requirement\'s state is derived from the runs bound to a formal Release:\nverified, failing, incomplete, or not-run, plus a stale flag and the\n(points_run / points_total) counts for its parameterized test points.\n\nArgs:\n - project_id (string, UUID): The project to report on\n - release_id (string, UUID, optional): A formal Release (a baselines row with\n a release_version). Defaults to the project\'s CURRENT Release\n (release_status = \'released\'). Errors if the project has none.\n - include_gaps (boolean, optional, default false): Also return the not-run\n (test x unit x value) points for the Release.\n\nReturns:\n { release: {id, version, status}, readiness: {...roll-up counts...},\n requirements: [{requirement_id, state, stale, points_total, points_run}],\n gaps?: [{tc_id, asset, point_key}] }\n An empty requirements array with a "hint" field means the projection has not\n been rebuilt for this project yet, NOT that everything is unverified.\n\nExamples:\n - "Are we ready to ship 2.0?" → atoms_verification_status(project_id)\n - "What\'s still not run for release R?" → atoms_verification_status(project_id, release_id="...", include_gaps=true)',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),release_id:o.z.string().uuid().optional().describe("Formal Release (baselines row) UUID; defaults to the project's current Release"),include_gaps:o.z.boolean().default(!1).describe("Include the not-run (test x unit x value) points for the Release")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_verification_status",async e=>{const{verificationStatusHandler:t}=await Promise.resolve().then(()=>(Dr(),Or));return t(e)})),Wa("atoms_get_history",{title:"Get Item Change History",description:"Audit trail for an item — who changed what, when, and whether it was human or AI.\n\nShows actor attribution (user vs mcp_<client>) and session grouping.\n\nArgs:\n - project_id (string, UUID): The project containing the item\n - item_id (string): Item ID\n - limit (number, optional): Max entries (default 20, max 100)\n\nReturns:\n Change entries with actor, session_id, event_type, changed_at, fields_changed.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID"),limit:o.z.number().int().min(1).max(100).default(20).describe("Max entries (default 20)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_get_history",async e=>{const{getHistoryHandler:t}=await Promise.resolve().then(()=>(Cr(),Hr));return t(e)})),Za({appName:"mermaid",htmlFile:"mermaid-app.html",toolName:"atoms_export_mermaid",title:"Export Mermaid Diagram",description:"Generate a Mermaid diagram of the requirement/test hierarchy.\n\nOutput is paste-ready for markdown docs. Shows parent-child relationships\nand requirement-to-test-case verification links.\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive pan/zoom diagram.\nFalls back to Mermaid text for non-UI clients.\n\nArgs:\n - project_id (string, UUID): The project to visualize\n - root_item_id (string, optional): Start node (default: all roots)\n - depth (number, optional): Max depth (default 3, max 10)\n - include_tests (boolean, optional): Show test case links (default true)\n - baseline_id (string, UUID, optional): render the graph at that baseline's moment\n - as_of (string ISO 8601, optional): render the graph at that moment\n baseline_id and as_of are mutually exclusive.\n\nReturns:\n Mermaid graph string.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),root_item_id:o.z.string().max(20).optional().describe("Root item ID to start from"),depth:o.z.number().int().min(1).max(10).default(3).describe("Max depth"),include_tests:o.z.boolean().default(!0).describe("Include test case links"),baseline_id:o.z.string().uuid().optional().describe("Render the graph as of this baseline's snapshot moment"),as_of:o.z.string().datetime().optional().describe("Render the graph as of this ISO 8601 moment")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Xa("atoms_export_mermaid",async e=>{const{exportMermaidHandler:t}=await Promise.resolve().then(()=>(Fr(),Nr));return t(e)})}),Wa("atoms_create_item",{title:"Create ATOMS Item",description:'Create a new requirement, test case, or note in a project.\n\nRequires editor or admin role. Changes are logged with AI actor attribution.\n\nArgs:\n - project_id (string, UUID): Target project\n - type (string): requirement|test-case|note\n - title (string): Item title (max 500 chars)\n - body (string, optional): Rich text body\n - summary (string, optional): Brief summary\n - domains (string[], optional): Domain tags (a tag flagged as a function is not a domain and is rejected)\n - level (string, optional): System|Subsystem|Component\n - parent_ids (string[], optional): Parent item IDs to link\n - fields (object, optional): Project-field values, e.g. {"Verification Method": "Design Review"}. Keys must be defined via atoms_create_field first and values must match each field type.\n\nReturns:\n Created item with generated ID (e.g., "REQ-058")\n\nSide effects:\n - Logs to change_history with actor=\'mcp_<client>\'\n - Creates relationships if parent_ids provided',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the target project"),type:o.z.enum(["requirement","test-case","note"]).describe("Item type"),title:o.z.string().min(1).max(500).describe("Item title"),body:o.z.string().max(5e4).optional().describe("Rich text body"),summary:o.z.string().max(2e3).optional().describe("Brief summary"),domains:o.z.array(o.z.string().max(64)).max(20).optional().describe("Domain tags"),level:o.z.string().max(32).optional().describe("System|Subsystem|Component"),parent_ids:o.z.array(o.z.string().max(20)).max(50).optional().describe("Parent item IDs to link"),fields:o.z.record(o.z.string().max(60),o.z.string().max(1e4)).optional().describe("Project-field values keyed by defined field name"),echo:o.z.boolean().optional().describe("false → lean {id,type} response, saves ~580 tokens")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_create_item",async e=>{const{createItemHandler:t}=await Promise.resolve().then(()=>(Li(),$i));return t(e)})),Qa={steps:o.z.array(o.z.object({id:o.z.string().describe("Stable step id within the item"),instruction:o.z.string().describe("What the tester does"),test_data:o.z.string().optional().describe("Optional test data for the step"),expected:o.z.string().describe("Expected result")}).passthrough()).optional().describe("Test-case script steps: array of {id, instruction, test_data?, expected}. Max 50 steps, enforced by the DB trigger."),params:o.z.array(o.z.object({name:o.z.string().describe("Parameter name; steps reference it as {name}"),unit:o.z.string().optional().describe("Optional unit (e.g. km/h, V, m)"),values:o.z.array(o.z.union([o.z.string(),o.z.number()])).describe("Value set the test sweeps")}).passthrough()).optional().describe("Matrix parameters: array of {name, unit, values[]}. Matrix points (product of value-set sizes) capped at 64 by the DB trigger.")},Wa("atoms_update_item",{title:"Update ATOMS Item",description:'Update an existing item\'s fields. Only provided fields are changed.\n\nRequires editor or admin role. Logs old/new data diff to change history.\n\nArgs:\n - project_id (string, UUID): Project containing the item\n - item_id (string): Item to update\n - title, body, summary, domains, level, status: Fields to update (all optional) (a tag flagged as a function is not a domain and is rejected)\n - fields (object, optional): Project-field values, e.g. {"Verification Method": "Design Review"}. Keys must be defined via atoms_create_field; merged per key, "" clears a key; non-empty values must match each field type\n - steps (array, optional): Test-case script steps [{id, instruction, test_data?, expected}]. Max 50 steps (DB-enforced)\n - params (array, optional): Matrix parameters [{name, unit, values[]}]. Matrix points capped at 64 (DB-enforced)\n - expected_updated_at (string, optional): Pass metadata.updated_at from atoms_get_item to reject stale writes\n\nReturns:\n Updated item.',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).optional().describe("Item ID (single form)"),title:o.z.string().min(1).max(500).optional().describe("New title"),body:o.z.string().max(5e4).optional().describe("New body"),summary:o.z.string().max(2e3).optional().describe("New summary"),domains:o.z.array(o.z.string().max(64)).max(20).optional().describe("New domain tags (a tag flagged as a function is not a domain and is rejected)"),level:o.z.string().max(32).optional().describe("New level"),status:o.z.enum(["passed","failed","blocked","not-run"]).optional().describe("Test case status"),fields:o.z.record(o.z.string().max(60),o.z.string().max(1e4)).optional().describe('Project-field values keyed by defined field name; "" clears a key'),...Qa,expected_updated_at:lt.optional().describe("metadata.updated_at value from atoms_get_item; rejects stale writes"),echo:o.z.boolean().optional().describe("false → lean {id,updated_fields} response, saves ~580 tokens"),reason:o.z.string().max(500).optional().describe("Change rationale, persisted in audit history"),updates:o.z.array(o.z.object({item_id:o.z.string().min(1).max(20),title:o.z.string().min(1).max(500).optional(),body:o.z.string().max(5e4).optional(),summary:o.z.string().max(2e3).optional(),domains:o.z.array(o.z.string().max(64)).max(20).optional(),level:o.z.string().max(32).optional(),status:o.z.enum(["passed","failed","blocked","not-run"]).optional(),fields:o.z.record(o.z.string().max(60),o.z.string().max(1e4)).optional(),...Qa,expected_updated_at:lt.optional()})).optional().describe("Array form: update many items in one call"),idempotency_key:o.z.string().max(128).optional().describe("Safe retry key (24h TTL)"),continue_on_error:o.z.boolean().optional().describe("Allow partial success (default false = atomic)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_update_item",async e=>{const{updateItemHandler:t}=await Promise.resolve().then(()=>(Yi(),Bi));return t(e)})),Wa("atoms_delete_item",{title:"Delete ATOMS Item",description:'Soft-delete an item (sets deleted_at, preserves for audit trail).\n\nRequires editor or admin role. The item is never truly removed.\n\nWhen ATOMS_MCP_REQUIRE_CONFIRMATION is set on the server, this tool uses a\ntwo-step flow: the first call returns a preview + confirmation_token; the\nsecond call (with the token) executes. Tokens expire in 60s and are bound\nto (tool, project_id, item_id).\n\nArgs:\n - project_id (string, UUID): Project containing the item\n - item_id (string): Item to delete\n - confirmation_token (string, optional): Token from a prior preview call\n\nReturns:\n Confirmation with deleted item summary, or { status: "confirmation_required",\n preview, confirmation_token } when the confirmation gate is active.',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID to soft-delete"),confirmation_token:o.z.string().max(500).optional().describe("Token from a prior preview call (only used when ATOMS_MCP_REQUIRE_CONFIRMATION is set)")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_delete_item",async e=>{const{deleteItemHandler:t}=await Promise.resolve().then(()=>(on(),an));return t(e)})),Wa("atoms_restore_item",{title:"Restore ATOMS Item",description:'Undo a soft-delete — restores an item that was previously deleted with atoms_delete_item.\n\nOnly works on items that have been soft-deleted (still in the database with deleted_at set).\nHas no effect if the item is not deleted. Logs the restoration to change_history.\n\nArgs:\n - project_id (string, UUID): Project containing the item\n - item_id (string): ID of the deleted item to restore\n\nReturns:\n Confirmation with the restored item\'s title and type.\n\nExamples:\n - "Restore the deleted requirement REQ-042" → atoms_restore_item(project_id, "REQ-042")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().max(256).describe("ID of the soft-deleted item to restore")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_restore_item",async e=>{const{restoreItemHandler:t}=await Promise.resolve().then(()=>(ln(),dn));return t(e)})),Wa("atoms_link_items",{title:"Link ATOMS Items",description:"Add or remove relationships between items.\n\nSupports: parent, child, related, verifies, verified_by.\nUpdates both items' JSONB data and the shadow table.\n\nArgs:\n - project_id (string, UUID): Project containing both items\n - from_id (string): Source item\n - to_id (string): Target item\n - type (string): parent|child|related|verifies|verified_by\n - action (string): add|remove\n - expected_from_updated_at / expected_to_updated_at (string, optional): pass metadata.updated_at values from atoms_get_item to reject stale link commands\n\nReturns:\n Updated relationship state for both items.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),from_id:o.z.string().min(1).max(20).optional().describe("Source item ID (single form)"),to_id:o.z.string().min(1).max(20).optional().describe("Target item ID (single form)"),type:o.z.enum(["parent","child","related","verifies","verified_by"]).optional().describe("Relationship type"),action:o.z.enum(["add","remove"]).optional().describe("Add or remove"),expected_from_updated_at:lt.optional().describe("metadata.updated_at for from_id from atoms_get_item"),expected_to_updated_at:lt.optional().describe("metadata.updated_at for to_id from atoms_get_item"),echo:o.z.boolean().optional().describe("false → lean response"),reason:o.z.string().max(500).optional().describe("Change rationale, persisted in audit history"),operations:o.z.array(o.z.object({action:o.z.enum(["add","remove"]),from_id:o.z.string().min(1).max(20),to_id:o.z.string().min(1).max(20),type:o.z.enum(["parent","child","related","verifies","verified_by"]),expected_from_updated_at:lt.optional(),expected_to_updated_at:lt.optional()})).optional().describe("Array form: batch relationship ops. Always atomic with DAG cycle detection."),idempotency_key:o.z.string().max(128).optional().describe("Safe retry key (24h TTL)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_link_items",async e=>{const{linkItemsHandler:t}=await Promise.resolve().then(()=>(un(),mn));return t(e)})),Za({appName:"import",htmlFile:"import-app.html",toolName:"atoms_bulk_import",title:"Bulk Import ATOMS Items",description:"Bulk create multiple items in a single tool call. Essential for AI agents\nthat generate 20+ requirements at once.\n\nChecks write access once, generates sequential IDs, batch inserts all items,\nand reports per-item errors without aborting the entire batch.\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive results table.\nFalls back to JSON for non-UI clients.\n\nArgs:\n - project_id (string, UUID): Target project\n - items (array): Up to 100 items to create, each with:\n - type (string): requirement|test-case|note\n - title (string): Item title (max 500 chars)\n - body (string, optional): Rich text body\n - summary (string, optional): Brief summary\n - domains (string[], optional): Domain tags (a tag flagged as a function is not a domain and is rejected)\n - level (string, optional): System|Subsystem|Component\n - parent_id (string, optional): Parent item ID to link\n\nReturns:\n { created: number, items: [{ id, title, type }], errors: [] }\n\nLimits:\n - Maximum 100 items per call\n - If any item fails, others still succeed — errors reported separately\n\nSide effects:\n - Logs to change_history with actor='mcp_<client>' for each created item\n - Creates parent relationships for items with parent_id",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the target project"),items:o.z.array(o.z.object({type:o.z.enum(["requirement","test-case","note"]).describe("Item type"),title:o.z.string().min(1).max(500).describe("Item title"),body:o.z.string().max(5e4).optional().describe("Rich text body"),summary:o.z.string().max(2e3).optional().describe("Brief summary"),domains:o.z.array(o.z.string().max(64)).max(20).optional().describe("Domain tags"),level:o.z.string().max(32).optional().describe("System|Subsystem|Component"),parent_id:o.z.string().max(20).optional().describe("Parent item ID to link")})).min(1).max(100).describe("Items to create (1-100)"),confirmation_token:o.z.string().max(500).optional().describe("Token from a prior preview call (only used when ATOMS_MCP_REQUIRE_CONFIRMATION is set)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1},handler:Xa("atoms_bulk_import",async e=>{const{bulkImportHandler:t}=await Promise.resolve().then(()=>(yn(),fn));return t(e)})}),Ga={point:o.z.record(o.z.string(),o.z.union([o.z.string(),o.z.number()])).optional().describe('Matrix point this run executed, e.g. {"speed": 40}'),release_id:o.z.string().uuid().optional().describe("Formal Release to bind this run to (a baseline with a release_version)"),build:o.z.string().optional().describe("Free-text build label"),environment:o.z.string().optional().describe("Structured environment field, distinct from build"),tooling:o.z.string().optional().describe("Structured tooling field, distinct from build"),steps_rev:o.z.string().optional().describe("Item revision id the run's steps were pinned to"),step_results:o.z.array(o.z.object({step_id:o.z.string().describe("Step id from data.steps"),status:o.z.enum(["passed","failed","blocked","skipped"]).describe("Per-step status"),actual:o.z.string().optional().describe("Actual-result note"),evidence_url:o.z.string().optional().describe("Evidence URL (validated server-side)")}).passthrough()).optional().describe("Per-step results [{step_id, status, actual?, evidence_url?}]. When present the run verdict is derived server-side and the top-level result is ignored.")},Wa("atoms_record_test_result",{title:"Record Test Result",description:"Record a pass/fail/blocked result for a test case.\n\nAppends to canonical items.data.runs and projects test_results from that\nhistory. Use atoms_get_item to see all results.\n\nArgs:\n - project_id (string, UUID): Project containing the test case\n - item_id (string): Test case ID (e.g., \"TC-001\")\n - result (string): passed|failed|blocked|not-run\n - note (string, optional): Reason or comment for this result\n - asset (string, optional): Asset identifier this run was executed against\n (VIN, module ID, lot number, serial number, etc). Max 200 chars.\n Auto-trimmed; empty/whitespace is treated as omitted. If the asset\n name does not yet exist in the project, it is auto-registered.\n - point, release_id, build, environment, tooling, steps_rev (optional):\n run metadata. release_id must be a formal Release (a baseline with a\n release_version). All validated server-side.\n - step_results (array, optional): per-step outcomes for a stepped run.\n When provided, the verdict is derived server-side from the steps.\n\nReturns:\n Recorded result with timestamp. When asset is provided, also returns\n asset_id and asset_created.\n\nSide effects:\n - Appends to items.data.runs through save_item_with_revision\n - Projects public.test_results from items.data.runs\n - Inserts into assets table if asset name is new in this project\n - Logs to change_history with actor='mcp_<client>'",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Test case ID (e.g., TC-001)"),result:o.z.enum(["passed","failed","blocked","not-run"]).describe("Test result"),note:o.z.string().max(500).optional().describe("Reason or comment for this result"),asset:o.z.string().max(200).optional().describe("Asset identifier this run was executed against (VIN, module ID, lot, etc). Auto-registered if new."),...Ga},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_record_test_result",async e=>{const{recordTestResultHandler:t}=await Promise.resolve().then(()=>(vn(),wn));return t(e)})),Wa("atoms_record_test_results",{title:"Record Test Results (bulk)",description:'Record many runs on one test case in a single atomic call.\n\nOptimized for multi-asset campaigns. Each entry can have its own asset and\nresult. Asset lookup-or-create happens per entry; new asset names are\nauto-registered. Runs are appended to canonical items.data.runs, then\ntest_results is projected from that history. The whole call is one DB\ntransaction; any entry failure rolls back the rest.\n\nUse the singular atoms_record_test_result for one-off runs.\n\nArgs:\n - project_id (string, UUID): Project containing the test case\n - item_id (string): Test case ID (e.g., "TC-001")\n - results (array, 1-100 entries): Each entry has:\n - asset (string, optional): Asset identifier (VIN, module ID, lot)\n - result (string, required): passed|failed|blocked|not-run\n - note (string, optional): Run note\n - date (string, optional): ISO 8601 datetime, default now()\n - point, release_id, build, environment, tooling, steps_rev (optional):\n run metadata; release_id must be a formal Release. Server-validated.\n - step_results (array, optional): per-step outcomes; when present the\n verdict is derived server-side from the steps.\n\nReturns:\n Per-entry outcomes with asset_id, asset_created, run_at, ok flags.\n\nSide effects:\n - Appends to items.data.runs through save_item_with_revision\n - Projects public.test_results from items.data.runs\n - Inserts new rows into assets for any asset name not already registered\n - Logs a single change_history entry summarizing the batch',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Test case ID (e.g., TC-001)"),results:o.z.array(o.z.object({asset:o.z.string().max(200).optional().describe("Asset identifier this run was executed against. Auto-registered if new."),result:o.z.enum(["passed","failed","blocked","not-run"]).describe("Test result"),note:o.z.string().max(500).optional().describe("Run note"),date:o.z.string().optional().describe("ISO 8601 datetime (default: now())"),...Ga})).min(1).max(100).describe("1 to 100 result entries on this test case")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_record_test_results",async e=>{const{recordTestResultsBulkHandler:t}=await Promise.resolve().then(()=>(An(),jn));return t(e)})),Za({appName:"trace",htmlFile:"trace-app.html",toolName:"atoms_trace",title:"Trace Item Relationships",description:'Walk the traceability graph from a starting item.\n\nAnswers questions like "which requirements does TC-003 verify?" or\n"if I change REQ-001, what\'s affected downstream?"\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive graph visualization.\nFalls back to flat list for non-UI clients.\n\nArgs:\n - project_id (string, UUID): Project containing the item\n - item_id (string): Starting item ID\n - direction (string): upstream|downstream|both\n - upstream: follow parent/verifies links (dependencies)\n - downstream: follow child/verified_by links (dependents)\n - both: trace in both directions\n - depth (number, optional): Max traversal depth (default 5, max 10)\n - relationship_types (string[], optional): Filter to specific types (parent, child, related, verifies, verified_by, mitigated_by, mitigates)\n\nReturns:\n { root, direction, items: [{ id, title, type, relationship, depth }], total_count }\n\nExamples:\n - "What does TC-003 verify?" → atoms_trace(project_id, "TC-003", "upstream")\n - "What\'s affected by REQ-001?" → atoms_trace(project_id, "REQ-001", "downstream")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Starting item ID"),direction:o.z.enum(["upstream","downstream","both"]).describe("Traversal direction"),depth:o.z.number().int().min(1).max(10).default(5).describe("Max traversal depth (default 5)"),relationship_types:o.z.array(o.z.enum(["parent","child","related","verifies","verified_by","mitigated_by","mitigates"])).optional().describe("Filter to specific relationship types")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Xa("atoms_trace",async e=>{const{traceHandler:t}=await Promise.resolve().then(()=>(Hn(),zn));return t(e)})}),Wa("atoms_list_assets",{title:"List Project Assets",description:"List asset identifiers registered in a project.\n\nAssets are free-form per-instance IDs (VINs, module names, lot numbers,\nserial numbers) that test runs are tagged against. They are auto-registered\nthe first time they appear on a run via atoms_record_test_result.\n\nArgs:\n - project_id (string, UUID): Project to list assets for\n - include_archived (boolean, optional): Include archived assets (default false)\n\nReturns:\n { assets: [{ id, name, archived_at, created_at }], total }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),include_archived:o.z.boolean().optional().describe("Include archived assets (default false)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_list_assets",async e=>{const{listAssetsHandler:t}=await Promise.resolve().then(()=>(qn(),Un));return t(e)})),Wa("atoms_list_variables",{title:"List Project Variables",description:"List all parameterized variables defined in a project.\n\nVariables are shared values (e.g., backup_camera_latency = 2s) that can be\nreferenced in requirement bodies as {variable_name}.\n\nArgs:\n - project_id (string, UUID): Project to list variables for\n - baseline_id (string, UUID, optional): list variables as they were at that baseline\n - as_of (string ISO 8601, optional): list variables as they were at that moment\n - limit (number, optional): max results (default 50, max 200)\n - offset (number, optional): pagination offset (default 0)\n\nReturns:\n { variables: [{ id, name, value, unit, description }], total }, meta: { total_count, limit, offset, has_more }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),baseline_id:o.z.string().uuid().optional().describe("Optional baseline UUID for time-travel reads"),as_of:o.z.string().datetime().optional().describe("Optional ISO timestamp for time-travel reads"),limit:o.z.number().int().min(1).max(200).default(50).describe("Max results (default 50, max 200)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset (default 0)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_list_variables",async e=>{const{listVariablesHandler:t}=await Promise.resolve().then(()=>(Bn(),Tn));return t(e)})),Wa("atoms_get_variable",{title:"Get Project Variable",description:'Get a specific variable by name, including which items reference it.\n\nArgs:\n - project_id (string, UUID): Project containing the variable\n - variable_name (string): Variable name (e.g., "backup_camera_latency")\n - baseline_id (string, UUID, optional): get the variable as it was at that baseline\n - as_of (string ISO 8601, optional): get the variable as it was at that moment\n\nReturns:\n { variable, referenced_by: [{ id, title, type }], reference_count }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),variable_name:o.z.string().min(1).max(64).describe("Variable name"),baseline_id:o.z.string().uuid().optional().describe("Optional baseline UUID for time-travel reads"),as_of:o.z.string().datetime().optional().describe("Optional ISO timestamp for time-travel reads")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_get_variable",async e=>{const{getVariableHandler:t}=await Promise.resolve().then(()=>(Bn(),Tn));return t(e)})),Wa("atoms_update_variable",{title:"Update Project Variable",description:"Update a variable's value, unit, or description.\n\nArgs:\n - project_id (string, UUID): Project containing the variable\n - variable_name (string): Variable name\n - value (string, optional): New value\n - unit (string, optional): Unit abbreviation (e.g., 's', 'Hz')\n - description (string, optional): Human-readable description\n\nReturns:\n { variable }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),variable_name:o.z.string().min(1).max(64).describe("Variable name"),value:o.z.string().max(500).optional().describe("New value"),unit:o.z.string().max(32).optional().describe("Unit abbreviation"),description:o.z.string().max(2e3).optional().describe("Description")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_update_variable",async e=>{const{updateVariableHandler:t}=await Promise.resolve().then(()=>(Bn(),Tn));return t(e)})),Wa("atoms_create_variable",{title:"Create Project Variable",description:'Create one or many parameterized variables for a project.\n\nSingle form: provide name + value.\nArray form: provide variables[] for bulk creation (one atomic INSERT).\n\nVariables can then be embedded in requirement bodies as {variable_name}.\n\nArgs (single form):\n - project_id (string, UUID): Project to add the variable to\n - name (string): Variable name, letters, digits, underscores; must start with letter/underscore\n - value (string): Initial value (e.g., "100", "true", "nominal")\n - unit (string, optional): Unit abbreviation (e.g., "Hz", "ms", "m/s²")\n - description (string, optional): Human-readable description\n - echo (bool, optional): false → lean {name} response (default true)\n\nArgs (array form):\n - project_id (string, UUID): Project UUID\n - variables[]: Array of { name, value, unit?, description? }\n - echo (bool, optional): false → lean {name} list (default true)\n - idempotency_key (string, optional): Dedup key\n\nReturns (single): { variable, message }\nReturns (array): { batch_id, created, variables, message }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).optional().describe("Variable name (single form)"),value:o.z.string().min(1).max(500).optional().describe("Initial value (single form)"),unit:o.z.string().max(32).optional().describe("Unit abbreviation"),description:o.z.string().max(2e3).optional().describe("Description"),echo:o.z.boolean().optional().describe("false → lean response (default true)"),variables:o.z.array(o.z.object({name:o.z.string().min(1).max(64).describe("Variable name"),value:o.z.string().min(1).max(500).describe("Initial value"),unit:o.z.string().max(32).optional().describe("Unit abbreviation"),description:o.z.string().max(2e3).optional().describe("Description")})).optional().describe("Array form: batch variable creation. Atomic — all or none."),idempotency_key:o.z.string().max(128).optional().describe("Dedup key for retries")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_create_variable",async e=>{const{createVariableHandler:t}=await Promise.resolve().then(()=>(Bn(),Tn));return t(e)})),Wa("atoms_delete_variable",{title:"Delete Project Variable",description:"Delete a project variable. Refuses by default if any items reference it.\n\nArgs:\n - project_id (string, UUID): Project containing the variable\n - name (string): Variable name to delete\n - force (bool, optional): Delete even if items still reference it (default false)\n\nReturns:\n { deleted, name, referenced_by_items, warning? }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).describe("Variable name to delete"),force:o.z.boolean().optional().describe("Delete even if items reference it (default false)"),confirmation_token:o.z.string().max(500).optional().describe("Token from a prior preview call (only used when ATOMS_MCP_REQUIRE_CONFIRMATION is set)")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_delete_variable",async e=>{const{deleteVariableHandler:t}=await Promise.resolve().then(()=>(Bn(),Tn));return t(e)})),Wa("atoms_list_domains",{title:"List Project Domains",description:"List all domain tags registered in a project's taxonomy, with item counts.\n\nArgs:\n - project_id (string, UUID): Project to inspect\n\nReturns:\n { domains: [{ name, item_count }], total }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_list_domains",async e=>{const{listDomainsHandler:t}=await Promise.resolve().then(()=>(ea(),Jn));return t(e)})),Wa("atoms_create_domain",{title:"Create Project Domain",description:'Register a new domain tag in the project taxonomy.\n\nOnce created, items can be tagged with this domain via atoms_create_item or atoms_update_item.\n\nArgs:\n - project_id (string, UUID): Project to add the domain to\n - name (string): Domain name (lowercased automatically, e.g., "safety", "can-bus")\n\nReturns:\n { domain: { name }, message }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).describe("Domain name")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_create_domain",async e=>{const{createDomainHandler:t}=await Promise.resolve().then(()=>(ea(),Jn));return t(e)})),Wa("atoms_list_levels",{title:"List Project Levels",description:"List the project's level taxonomy in order, with each level's L# (positional index) and item count.\n\nArgs:\n - project_id (string, UUID): Project to list levels for\n\nReturns:\n { levels: [{ name, prefix, item_count }], total }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_list_levels",async e=>{const{listLevelsHandler:t}=await Promise.resolve().then(()=>(di(),Wr));return t(e)})),Wa("atoms_create_level",{title:"Create Project Level",description:'Register a new level in the project taxonomy so items can be tagged with it and it shows in the Strata view. Appended to the ordered level list; its L# is the next index. Names are user-defined labels (lowercased automatically); matching is case-insensitive.\n\nArgs:\n - project_id (string, UUID): Project to add the level to\n - name (string): Level name, e.g. "feature", "system", "subsystem"\n\nReturns:\n { level: { name, prefix }, message }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).describe("Level name (user-defined label)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_create_level",async e=>{const{createLevelHandler:t}=await Promise.resolve().then(()=>(di(),Wr));return t(e)})),Wa("atoms_list_fields",{title:"List Project Fields",description:'List the project\'s custom field definitions (project-scoped key-value slots on items, e.g. "Verification Method"), with counts of items carrying a value.\n\nField values are set per item via atoms_create_item / atoms_update_item fields.\n\nArgs:\n - project_id (string, UUID): Project to inspect\n\nReturns:\n { fields: [{ name, type, options, item_count }], total }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_list_fields",async e=>{const{listFieldsHandler:t}=await Promise.resolve().then(()=>(Pi(),Si));return t(e)})),Wa("atoms_create_field",{title:"Create Project Field",description:'Define a project custom field so items can carry a value for it (shown as a Matrix column, e.g. "Verification Method").\n\nThe name keeps its casing; uniqueness is case-insensitive. Type is one of text, long, bool, date, person, select, number, link. Select fields require options. Field definitions never carry visibility rules, permissions, or workflow logic.\n\nArgs:\n - project_id (string, UUID): Project to define the field in\n - name (string): Field name, 1-60 characters (e.g. "Verification Method", "Essential Output?")\n - type (string, optional): Defaults to text\n - options (string[], optional): Required when type=select\n - scope (string, optional): project (default) or organization (org admin only)\n\nReturns:\n { field: { name, type, options }, message }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(60).describe("Field name (display name, 1-60 chars)"),type:o.z.enum(["text","long","bool","date","person","select","number","link"]).optional().describe("Field type, defaults to text"),options:o.z.array(o.z.string().min(1).max(120)).max(100).optional().describe("Allowed values for select fields"),scope:o.z.enum(["project","organization"]).optional().describe("Create in this project or copy to every project in the organization")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_create_field",async e=>{const{createFieldHandler:t}=await Promise.resolve().then(()=>(Pi(),Si));return t(e)})),Wa("atoms_delete_field",{title:"Delete Project Field",description:"Delete a project field definition. Existing item values are left in item JSON but no longer render as Matrix columns until a matching field is created again.\n\nArgs:\n - project_id (string, UUID): Project containing the field\n - name (string): Field name to delete",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(60).describe("Field name")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_delete_field",async e=>{const{deleteFieldHandler:t}=await Promise.resolve().then(()=>(Pi(),Si));return t(e)})),Wa("atoms_reorder_fields",{title:"Reorder Project Fields",description:"Reorder project field definitions. Definition order drives the Column Picker listing and a fresh user's Matrix column order.\n\nOrdering only: no definition is added, dropped, renamed, or retyped, and no item value moves. Use this instead of deleting and recreating definitions to change their order.\n\nArgs:\n - project_id (string, UUID): Project containing the fields\n - names (string[]): Every existing field name exactly once, in the order you want them. A list that is not a permutation of the current names is refused, not partially applied.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),names:o.z.array(o.z.string().min(1).max(60)).describe("Every existing field name exactly once, in the desired order")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_reorder_fields",async e=>{const{reorderFieldsHandler:t}=await Promise.resolve().then(()=>(Pi(),Si));return t(e)})),Wa("atoms_update_domain",{title:"Rename Project Domain",description:"Rename a domain tag. Updates the taxonomy and propagates to all tagged items.\n\nUse dry_run=true first to see how many items will be affected before committing.\n\nArgs:\n - project_id (string, UUID): Project containing the domain\n - name (string): Current domain name\n - new_name (string): New domain name\n - dry_run (bool, optional): If true, return impact count without making changes (default false)\n\nReturns (dry_run=false):\n { domain: { name }, renamed_from, items_updated, message }\n\nReturns (dry_run=true):\n { dry_run: true, rename: { from, to }, items_affected, message }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).describe("Current domain name"),new_name:o.z.string().min(1).max(64).describe("New domain name"),dry_run:o.z.boolean().optional().describe("Preview impact without applying (default false)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_update_domain",async e=>{const{updateDomainHandler:t}=await Promise.resolve().then(()=>(ea(),Jn));return t(e)})),Wa("atoms_delete_domain",{title:"Delete Project Domain",description:"Delete a domain tag from the project taxonomy.\n\nRefuses by default if any items are tagged with it. With force=true, deletes the\ndomain and strips the tag from all items.\n\nArgs:\n - project_id (string, UUID): Project containing the domain\n - name (string): Domain name to delete\n - force (bool, optional): Strip from items and delete anyway (default false)\n\nReturns:\n { deleted, name, items_updated, message }",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(64).describe("Domain name to delete"),force:o.z.boolean().optional().describe("Strip from all items and delete (default false)"),confirmation_token:o.z.string().max(500).optional().describe("Token from a prior preview call (only used when ATOMS_MCP_REQUIRE_CONFIRMATION is set)")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_delete_domain",async e=>{const{deleteDomainHandler:t}=await Promise.resolve().then(()=>(ea(),Jn));return t(e)})),Za({appName:"summary",htmlFile:"summary-app.html",toolName:"atoms_project_summary",title:"Project Compliance Summary",description:'One-call project health and compliance dashboard.\n\nReturns item counts by type, test execution status, requirement coverage\n(overall and by domain), and recent change activity.\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive dashboard with charts.\nFalls back to JSON for non-UI clients.\n\nArgs:\n - project_id (string, UUID): Project to summarize\n\nReturns:\n { project_name, counts, test_status, coverage, coverage_by_domain, recent_changes, last_updated }\n\nExamples:\n - "Give me a compliance snapshot" → atoms_project_summary(project_id)\n - "How\'s our test coverage?" → atoms_project_summary(project_id)',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Xa("atoms_project_summary",async e=>{const{projectSummaryHandler:t}=await Promise.resolve().then(()=>(na(),ta));return t(e)})}),Za({appName:"browse",htmlFile:"browse-app.html",toolName:"atoms_browse",title:"Browse ATOMS Items",description:'View and filter items in an ATOMS project with a visual browser.\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive filterable list\nwith expandable item details. Falls back to JSON for non-UI clients.\n\nArgs:\n - project_id (string, UUID): The project to browse\n - type (string, optional): Filter by type (requirement, test-case, note, table)\n - domain (string, optional): Filter by domain tag\n - level (string, optional): Filter by level (System, Subsystem, Component)\n - query (string, optional): Full-text search query\n - limit (number, optional): Max results (default 25, max 100)\n - offset (number, optional): Pagination offset (default 0)\n\nReturns:\n { items: [...], filters: { domains, levels, types }, meta: { total_count, limit, offset, has_more } }\n\nExamples:\n - "Show me the requirements" → atoms_browse(project_id, type="requirement")\n - "Browse safety items" → atoms_browse(project_id, domain="Safety")\n - "Find braking requirements" → atoms_browse(project_id, query="braking")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),type:o.z.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),domain:o.z.string().max(64).optional().describe("Filter by domain tag"),level:o.z.string().max(32).optional().describe("Filter by level (System, Subsystem, Component)"),query:o.z.string().max(1e3).optional().describe("Full-text search query"),limit:o.z.number().int().min(1).max(100).default(25).describe("Max results (default 25, max 100)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset (default 0)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Xa("atoms_browse",async e=>{const{browseHandler:t}=await Promise.resolve().then(()=>(ma(),aa));return t(e)})}),Wa("atoms_impact_analysis",{title:"Analyze Impact of Changing an Item",description:'Analyze the blast radius of changing a specific item.\n\nTraverses the relationship graph from the given item and returns every item that\nwould be affected by a change — with their types, depths, and full relationship paths.\n\nArgs:\n - project_id (string, UUID): Project containing the item\n - item_id (string): Item to analyze (e.g., "REQ-001")\n - direction (string, optional): "downstream" (default) | "upstream" | "both"\n - downstream: what this item affects (children, verified_by)\n - upstream: what affects this item (parents, verifies)\n - both: full bidirectional traversal\n - depth (integer, optional): Max traversal depth. Omit for full depth (all reachable nodes).\n - include_variable_refs (boolean, optional): Reserved for future variable-aware impact. Default true.\n\nReturns:\n { root: { item_id, title, type }, impacted_items: [{ item_id, title, type, depth, relationship_path }], summary: { total_impacted, by_type, max_depth_reached } }\n\nExamples:\n - "What breaks if I change REQ-001?" → atoms_impact_analysis(project_id, "REQ-001")\n - "What\'s upstream of TC-005?" → atoms_impact_analysis(project_id, "TC-005", direction="upstream")\n - "Show direct dependencies only" → atoms_impact_analysis(project_id, "REQ-001", depth=1)\n\nErrors:\n - "Item not found" → verify item_id exists in the project',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID to analyze (e.g., REQ-001)"),direction:o.z.enum(["downstream","upstream","both"]).default("downstream").describe("Traversal direction (default: downstream)"),depth:o.z.number().int().min(1).optional().describe("Max traversal depth. Omit for full depth."),include_variable_refs:o.z.boolean().default(!0).describe("Reserved for variable-aware impact (future). Default true.")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_impact_analysis",async e=>{const{impactAnalysisHandler:t}=await Promise.resolve().then(()=>(_a(),pa));return t(e)})),Wa("atoms_list_baselines",{title:"List ATOMS Baselines",description:"List named baselines (named project snapshots) for a project, newest first.\n\nA baseline is a labeled moment in time. Use atoms_create_baseline to make one,\natoms_diff_baselines to compare two, and atoms_restore_baseline to roll back.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),limit:o.z.number().int().min(1).max(100).default(50).describe("Max results (default 50, max 100)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_list_baselines",async e=>{const{listBaselinesHandler:t}=await Promise.resolve().then(()=>(Ia(),ha));return t(e)})),Wa("atoms_create_baseline",{title:"Create ATOMS Baseline",description:"Create a named baseline (snapshot label) at the current moment for a project.\n\nThe baseline records a name + timestamp. It does NOT copy item data; the project\nstate at that moment is reconstructed via temporal queries against item_revisions.\nNames must be unique per project (case-insensitive).",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),name:o.z.string().min(1).max(200).describe("Baseline name (1-200 chars, unique per project)"),description:o.z.string().max(2e3).optional().describe("Optional description (max 2000 chars)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_create_baseline",async e=>{const{createBaselineHandler:t}=await Promise.resolve().then(()=>(Ia(),ha));return t(e)})),Wa("atoms_lock_baseline",{title:"Lock ATOMS Baseline",description:"Lock a baseline so it becomes audit-grade immutable. Admin only. One-way: there is no unlock.\n\nAfter locking, the baseline's name, description, and snapshot_at cannot be changed,\nand it cannot be deleted. Use for regulatory submissions and DRBs.",inputSchema:{baseline_id:o.z.string().uuid().describe("UUID of the baseline to lock")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_lock_baseline",async e=>{const{lockBaselineHandler:t}=await Promise.resolve().then(()=>(Ia(),ha));return t(e)})),Wa("atoms_diff_baselines",{title:"Diff ATOMS Baselines",description:"Compute the diff between two baselines: which items were added, removed, or modified.\n\nReturns a summary plus a paginated items array. Pass detail=true to include\nper-item field-level diffs (slower for large projects).",inputSchema:{baseline_a_id:o.z.string().uuid().describe("UUID of the first (older) baseline"),baseline_b_id:o.z.string().uuid().describe("UUID of the second (newer) baseline"),detail:o.z.boolean().default(!1).describe("Include per-item field-level diffs (default false)"),limit:o.z.number().int().min(1).max(200).default(50).describe("Max items per page (default 50)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_diff_baselines",async e=>{const{diffBaselinesHandler:t}=await Promise.resolve().then(()=>(Ia(),ha));return t(e)})),Wa("atoms_restore_baseline",{title:"Restore from ATOMS Baseline",description:"Restore project state to a baseline. Admin only. Preview-by-default.\n\nCall with confirm=false (default) for a dry run that returns items_to_restore count.\nCall with confirm=true to execute: each item present at the baseline gets a new\nrevision matching its historical state, event_source='restore'. Items added AFTER\nthe baseline are NOT deleted. Always recoverable via further history.",inputSchema:{baseline_id:o.z.string().uuid().describe("UUID of the baseline to restore from"),confirm:o.z.boolean().default(!1).describe("Set true to execute; false (default) returns a preview")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_restore_baseline",async e=>{const{restoreBaselineHandler:t}=await Promise.resolve().then(()=>(Ia(),ha));return t(e)})),Wa("atoms_create_analysis",{title:"Create HARA / DFMEA Analysis",description:'Create a new safety analysis (HARA or DFMEA) with one empty row per seed.\n\nRequires editor or admin role. Structure matches analyses created in the ATOMS web app.\nA HARA is seeded from FUNCTIONS (tags flagged as functions), never from requirements: a\nrequirement is an output of the analysis. A DFMEA is seeded from requirements / design elements.\n\nArgs:\n - project_id (string, UUID): Target project\n - subtype (string): hara | dfmea\n - title (string, optional): Analysis title (default "New HARA" / "New DFMEA")\n - source_functions (string[], hara only, max 50): Function names to seed rows from. A name\n absent from the project\'s tags is registered as a function-flagged tag; matching is\n case-insensitive and trimmed. Rejected for dfmea.\n - source_req_ids (string[], dfmea only, max 50): Requirement IDs to seed rows from.\n Each must exist, be a plain requirement, and not itself be an analysis row. Rejected for hara.\n - revision (string, optional): Revision label (default "1.0")\n\nReturns:\n { id (e.g. "HARA-001" / "DFMEA-001"), subtype, title, revision, standard? ("ISO 26262" for hara),\n rows: [{ id, source_function }] (hara) | [{ id, source_req }] (dfmea),\n link_warnings?: [{ row_id, source_function | source_req, message }], warning? }\n rows lists every created row. If any row could not be attached to the analysis, it is\n named in link_warnings and warning explains the repair (atoms_link_items with type\n \'parent\', from_id=<row id>, to_id=<analysis id>); such rows will not appear in\n atoms_get_analysis until relinked.\n\nSide effects:\n - Creates the analysis parent item plus one row item (SG-nnn / FM-nnn) per seed\n - hara: registers new function names in the project\'s tags and function flags (metadata)\n - Links each row to the parent (dual-written to the relationship shadow table)\n - Logs each created item to change_history with actor=\'mcp_<client>\'',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the target project"),subtype:o.z.enum(["hara","dfmea"]).describe("Analysis subtype"),title:o.z.string().min(1).max(500).optional().describe("Analysis title"),source_functions:o.z.array(o.z.string().min(1).max(100)).max(50).optional().describe("hara only: function names to seed rows from (0-50); new names are registered as function-flagged tags"),source_req_ids:o.z.array(o.z.string().min(1).max(20)).max(50).optional().describe("dfmea only: requirement IDs to seed rows from (0-50)"),revision:o.z.string().min(1).max(32).optional().describe("Revision label (default 1.0)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Xa("atoms_create_analysis",async e=>{const{createAnalysisHandler:t}=await Promise.resolve().then(()=>(Ya(),Aa));return t(e)})),Wa("atoms_fill_row",{title:"Fill Analysis Row Fields",description:"Fill fields on one HARA / DFMEA analysis row (SG-nnn / FM-nnn).\n\nRequires editor or admin role. Written fields are marked as MCP-sourced so the\nweb app shows their provenance. The computed level (ASIL / RPN) is derived and\nnever stored: asil is never a writable key.\n\nArgs:\n - project_id (string, UUID): Project containing the row\n - row_id (string): Analysis row ID (e.g. \"SG-001\", \"FM-003\")\n - fields (object): Field name to value map. Allowed keys:\n hara: failure_mode, operating_scenario, hazard, assumptions, severity (S0-S3), exposure (E0-E4),\n controllability (C0-C3), safe_state, ftti, rationale, source_function, effect, title\n dfmea: failure_mode, cause, severity (1-10), occurrence (1-10), detection (1-10),\n rationale, effect\n 'effect' writes the row's long text body (the hazardous event for hara). dfmea failure_mode also\n becomes the row title. dfmea ratings accept numbers and are stored as strings.\n hara failure_mode: the standardized suggestions are No function, Loss of function, Partial function,\n Degradation of function, Misinterpretation of function (a suggestion; any text is accepted).\n hara source_function: the function the row analyzes, registered as a function-flagged tag if new.\n\nReturns:\n { row_id, subtype, written_fields, computed_level, asil_propagated_to? }\n\nSide effects:\n - Saves the row with stale-write protection and logs to change_history\n - hara only: if the row is linked and its computed ASIL changed, updates each\n linked requirement's asil / asil_source (each update is history-logged)",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),row_id:o.z.string().min(1).max(20).describe("Analysis row ID (e.g. SG-001, FM-003)"),fields:o.z.record(o.z.string().max(64),o.z.union([o.z.string().max(5e4),o.z.number()])).describe("Field name to value map (see description for allowed keys per subtype)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_fill_row",async e=>{const{fillRowHandler:t}=await Promise.resolve().then(()=>(Ya(),Aa));return t(e)})),Wa("atoms_get_analysis",{title:"Get HARA / DFMEA Analysis",description:'Get a full analysis view: every row with its computed level (ASIL / RPN) and\ngap / critical / stale classifications, plus summary counts.\n\nClassifications match the ATOMS web app exactly (same rules, same thresholds).\n\nArgs:\n - project_id (string, UUID): Project containing the analysis\n - analysis_id (string): Analysis ID (e.g. "HARA-001", "DFMEA-002")\n\nReturns:\n { analysis: { id, title, subtype, scheme, revision, standard },\n rows: [{ id, title, source_req, effect, <subtype fields incl. source_function / hazard / assumptions for hara>,\n computed_level, is_gap, gap_rule, is_critical, is_stale, mitigated_by, link_roles,\n approved, approved_at, mcp_fields }],\n counts: { rows, gaps, critical, stale, approved, linked } }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),analysis_id:o.z.string().min(1).max(20).describe("Analysis ID (e.g. HARA-001, DFMEA-002)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_get_analysis",async e=>{const{getAnalysisHandler:t}=await Promise.resolve().then(()=>(Ya(),Aa));return t(e)})),Wa("atoms_link_mitigation",{title:"Link Analysis Row to Mitigating Requirement",description:'Link a HARA / DFMEA row to the technical requirement that mitigates it.\n\nRequires editor or admin role.\n\nArgs:\n - project_id (string, UUID): Project containing both items\n - row_id (string): Analysis row ID (e.g. "SG-001", "FM-003")\n - req_id (string): Target requirement ID (must be a plain requirement, not an analysis row)\n - role (string, dfmea only, REQUIRED for dfmea): prevention | detection | mitigation.\n Must be omitted for hara rows.\n - override (boolean, optional, default false): hara only. When the target already\n carries a different asil, the call fails with a structured error\n (details.code=\'asil_conflict\') unless override=true; the override is\n history-logged like a dialog accept.\n\nReturns:\n { row_id, req_id, type: "mitigated_by", role, asil_written? }\n\nSide effects:\n - Adds the mitigated_by/mitigates relationship (JSONB + shadow table, one transaction)\n - hara only: writes the row\'s computed ASIL onto the target requirement\n (data.asil + data.asil_source) with a history entry recording previous/new values\n - dfmea: never modifies any field on the target requirement',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),row_id:o.z.string().min(1).max(20).describe("Analysis row ID (e.g. SG-001, FM-003)"),req_id:o.z.string().min(1).max(20).describe("Target requirement ID (e.g. REQ-042)"),role:o.z.enum(["prevention","detection","mitigation"]).optional().describe("Mitigation role. Required for dfmea rows; must be omitted for hara rows."),override:o.z.boolean().optional().describe("hara only: apply the row's ASIL over a conflicting existing value (history-logged)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_link_mitigation",async e=>{const{linkMitigationHandler:t}=await Promise.resolve().then(()=>(Ya(),Aa));return t(e)})),Wa("atoms_get_gaps",{title:"Get Analysis Gap Rows",description:'List only the gap rows of a HARA / DFMEA analysis, each naming the rule that matched.\n\nGap rules (identical to the web app):\n hara: unmitigated row with ASIL A-D ("asil <X> unmitigated")\n dfmea: unmitigated row with RPN >= 100 ("rpn >= 100") or severity >= 9 ("severity >= 9")\n\nArgs:\n - project_id (string, UUID): Project containing the analysis\n - analysis_id (string): Analysis ID (e.g. "HARA-001", "DFMEA-002")\n\nReturns:\n { analysis_id, subtype, gaps: [{ id, title, source_req, source_function, computed_level, rule }], count }',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),analysis_id:o.z.string().min(1).max(20).describe("Analysis ID (e.g. HARA-001, DFMEA-002)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Xa("atoms_get_gaps",async e=>{const{getGapsHandler:t}=await Promise.resolve().then(()=>(Ya(),Aa));return t(e)}))}});B(),$(),Ne(),M();var ns=l.createRequire("undefined"==typeof document?require("url").pathToFileURL(__filename).href:p&&"SCRIPT"===p.tagName.toUpperCase()&&p.src||new URL("index.cjs",document.baseURI).href)("../package.json"),as=process.argv.slice(2)[0];(async function(){switch(as){case"login":{const{login:e}=await Promise.resolve().then(()=>(Ye(),Le));try{const{email:t}=await e();process.stderr.write(`\n ✓ Authenticated as ${t}\n`),process.stderr.write(" ✓ Credentials saved to ~/.atoms/credentials.json\n\n"),process.stderr.write(" Next steps:\n"),process.stderr.write(" $ claude mcp add atoms -- npx -y @atoms-tech/atoms-mcp\n"),process.stderr.write("\n Or add to Claude Desktop (Settings → MCP → Edit Config):\n"),process.stderr.write(' {\n "mcpServers": {\n "atoms": {\n "command": "npx",\n "args": ["-y", "@atoms-tech/atoms-mcp"]\n }\n }\n }\n\n')}catch(e){process.stderr.write(`\n ✗ ${e instanceof Error?e.message:String(e)}\n\n`),process.exit(1)}break}case"whoami":{const{getValidToken:e}=await Promise.resolve().then(()=>(Re(),be));try{const{email:t,user_id:r}=await e();process.stderr.write(`\n ✓ Logged in as ${t}\n User ID: ${r}\n\n`)}catch(e){process.stderr.write(`\n ✗ Not authenticated: ${e instanceof Error?e.message:String(e)}\n Run: npx @atoms-tech/atoms-mcp login\n\n`),process.exit(1)}break}case"logout":{const{clearCredentials:e}=await Promise.resolve().then(()=>(oe(),J));await e(),process.stderr.write("Logged out. Credentials removed.\n"),process.stderr.write("Run 'npx @atoms-tech/atoms-mcp login' to authenticate again.\n");break}case"--version":case"-v":process.stderr.write(`@atoms-tech/atoms-mcp v${ns.version}\n`);break;case"--help":case"-h":process.stderr.write("ATOMS MCP Server — AI agent integration for requirements management\n\nUsage:\n npx @atoms-tech/atoms-mcp Start MCP server (stdio)\n npx @atoms-tech/atoms-mcp login Authenticate with ATOMS.tech\n npx @atoms-tech/atoms-mcp logout Switch account / clear credentials\n npx @atoms-tech/atoms-mcp whoami Show current user\n npx @atoms-tech/atoms-mcp --version Show version\n");break;default:{process.stderr.write("[atoms-mcp] Starting MCP server via stdio...\n");{const{getValidToken:e,readValidToken:t}=await Promise.resolve().then(()=>(Re(),be)),{runExclusiveAuth:r}=await Promise.resolve().then(()=>(he(),de)),{login:i}=await Promise.resolve().then(()=>(Ye(),Le));try{let n;try{n=(await e()).email}catch(e){process.stderr.write(`[atoms-mcp] Could not use the saved session: ${e instanceof Error?e.message:String(e)}\n`),process.stderr.write("[atoms-mcp] Starting login flow...\n");const a=async()=>{const e=await t();if(!e)throw new Error("no valid token yet");return{email:e.email}};n=(await r(a,async()=>({email:(await i()).email}))).email}process.stderr.write(`[atoms-mcp] Authenticated as ${n}\n`)}catch(e){process.stderr.write(`[atoms-mcp] Login failed: ${e instanceof Error?e.message:String(e)}\n[atoms-mcp] Starting server without auth. Tools will fail until you run: npx @atoms-tech/atoms-mcp login\n`)}}try{const t=await ze(),r=Ce(),i=await async function(e,t){const r=process.env.ATOMS_MCP_ORG_ID?.trim();if(r)return r;const{data:i,error:n}=await e.from("org_members").select("org_id, joined_at").eq("user_id",t).order("joined_at",{ascending:!0}).limit(1).maybeSingle();return n?(process.stderr.write(`[atoms-mcp] Could not resolve session org: ${n.message}\n`),null):i?.org_id??null}(t,r),n=await async function(e,t,r){if(!r)return{role:null,is_member:!1,effective:H};const{data:i,error:n}=await e.rpc("mcp_resolve_policy",{p_user_id:t,p_org_id:r});return n?(process.stderr.write(`[atoms-mcp] mcp_resolve_policy failed (${n.code}): ${n.message}. Falling back to fail-closed policy.\n`),{role:null,is_member:!1,effective:U}):function(e){if(!e||"object"!=typeof e)return{role:null,is_member:!1,effective:H};const t=e,r="string"==typeof t.role?t.role:null,i=!0===t.is_member,n=t.effective??{},a=(e,t)=>Array.isArray(e)?e.filter(e=>"string"==typeof e):t,s=(e,t)=>"boolean"==typeof e?e:t,o=n.project_scope,d=Array.isArray(o)&&o.length>0?o.filter(e=>"string"==typeof e):null;return{role:r,is_member:i,effective:{read_only:s(n.read_only,H.read_only),lockdown:s(n.lockdown,H.lockdown),block_destructive:s(n.block_destructive,H.block_destructive),block_bulk_import:s(n.block_bulk_import,H.block_bulk_import),cross_project_browse:s(n.cross_project_browse,H.cross_project_browse),allowed_toolsets:a(n.allowed_toolsets,H.allowed_toolsets),forbidden_tools:a(n.forbidden_tools,H.forbidden_tools),project_scope:d,require_confirmation_for:a(n.require_confirmation_for,H.require_confirmation_for)}}}(i)}(t,r,i);e={effective:n.effective,role:n.role,org_id:i},C=e.effective,q=e.org_id,n.is_member&&i?process.stderr.write(`[atoms-mcp] Org policy loaded: org=${i.slice(0,8)}… role=${n.role??"?"} read_only=${n.effective.read_only} lockdown=${n.effective.lockdown}\n`):process.stderr.write("[atoms-mcp] No org membership detected — running with permissive default policy.\n")}catch(e){process.stderr.write(`[atoms-mcp] Could not resolve session policy (${e instanceof Error?e.message:String(e)}). Running with permissive default — RLS still enforces row-level access.\n`)}process.stderr.write(`[atoms-mcp] Tool registry: ${function(){const e=L(),t=N(),r=[];r.push(e?"read-only":"read+write"),null===t?r.push("all toolsets"):(r.push(`toolsets=${[...t.allowed].sort().join(",")||"(none — only always-on tools)"}`),t.unknown.length>0&&r.push(`unknown=${t.unknown.join(",")}`));const i=process.env.ATOMS_MCP_PROJECT_ID?.trim();return i&&r.push(`project_scope=${i.slice(0,8)}…`),("1"===process.env.ATOMS_MCP_LOCKDOWN||"true"===process.env.ATOMS_MCP_LOCKDOWN)&&r.push("lockdown=on"),r.join(" | ")}()}\n`);const{server:t}=await Promise.resolve().then(()=>(is(),Ka)),r=new m.StdioServerTransport;await t.connect(r),process.stderr.write("[atoms-mcp] MCP server running. Waiting for tool calls...\n")}}var e})().catch(e=>{process.stderr.write(`[atoms-mcp] Fatal: ${e instanceof Error?e.message:String(e)}\n`),process.exit(1)});