@atoms-tech/atoms-mcp 0.5.0 → 0.6.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +11 -0
- package/dist/index.cjs +1 -1
- package/dist/index.js +1 -1
- package/package.json +1 -1
package/dist/index.js
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@@ -1,2 +1,2 @@
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#!/usr/bin/env node
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import e,{readFile as t,mkdir as r,writeFile as n,unlink as i}from"fs/promises";import{homedir as a}from"os";import o,{join as s}from"path";import{createClient as d}from"@supabase/supabase-js";import{registerAppTool as c,registerAppResource as l,RESOURCE_MIME_TYPE as m}from"@modelcontextprotocol/ext-apps/server";import{URL as p,fileURLToPath as u}from"url";import _,{randomUUID as f,randomBytes as h,createHash as g}from"crypto";import{McpServer as y}from"@modelcontextprotocol/sdk/server/mcp.js";import{z as b}from"zod";import{createServer as w}from"http";import{StdioServerTransport as v}from"@modelcontextprotocol/sdk/server/stdio.js";var j,x,S,k,I,E,T,O,H,C,D=Object.defineProperty,U=Object.getOwnPropertyNames,P=(e,t)=>function(){return e&&(t=(0,e[U(e)[0]])(e=0)),t},R=(e,t)=>{for(var r in t)D(e,r,{get:t[r],enumerable:!0})},q=P({"src/middleware/audit.ts"(){}}),A=P({"src/middleware/rate-limiter.ts"(){j=60,x=6e4,S=new Map}});function M(e){return C.get(e)}var $=P({"src/core/tool-catalog.ts"(){k=new Set(["atoms_status","atoms_list_projects"]),I=new Set(["atoms_create_item","atoms_update_item","atoms_delete_item","atoms_link_items","atoms_bulk_import","atoms_record_test_result","atoms_create_variable","atoms_update_variable","atoms_delete_variable","atoms_create_domain","atoms_update_domain","atoms_delete_domain"]),E=new Set(["atoms_delete_item","atoms_delete_variable","atoms_delete_domain"]),T=new Set(["atoms_bulk_import"]),O={items:["atoms_list_items","atoms_get_item","atoms_search","atoms_browse","atoms_get_history","atoms_create_item","atoms_update_item","atoms_delete_item","atoms_bulk_import"],traceability:["atoms_trace","atoms_link_items","atoms_export_mermaid","atoms_impact_analysis"],coverage:["atoms_get_coverage","atoms_record_test_result","atoms_project_summary"],variables:["atoms_list_variables","atoms_get_variable","atoms_create_variable","atoms_update_variable","atoms_delete_variable"],domains:["atoms_list_domains","atoms_create_domain","atoms_update_domain","atoms_delete_domain"]},H=Object.keys(O),C=new Map;for(const[e,t]of Object.entries(O))for(const r of t)C.set(r,e)}});function N(){const e=process.env.ATOMS_MCP_TOOLSETS?.trim();if(!e)return null;const t=e.split(",").map(e=>e.trim()).filter(Boolean);if(0===t.length)return null;const r=new Set,n=[];for(const e of t)H.includes(e)?r.add(e):n.push(e);return{allowed:r,unknown:n}}function V(){const e=process.env.ATOMS_MCP_READ_ONLY;return"1"===e||"true"===e?.toLowerCase()}function W(e){if(V()&&I.has(e))return!1;if(k.has(e))return!0;const t=N();if(null===t)return!0;const r=M(e);return!!r&&t.allowed.has(r)}var F,L,J,z=P({"src/middleware/tool-registry.ts"(){$()}});function B(){const e=process.env.ATOMS_MCP_PROJECT_ID?.trim();return e?F.test(e)?e:(L||(process.stderr.write(`[atoms-mcp] WARNING: ATOMS_MCP_PROJECT_ID="${e.slice(0,50)}" is not a valid UUID — scope ignored.\n`),L=!0),null):null}var Q,G,Y=P({"src/middleware/project-scope.ts"(){F=/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i,L=!1,J=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}}}}),K=P({"src/core/types.ts"(){Q={read_only:!1,lockdown:!1,block_destructive:!1,block_bulk_import:!1,cross_project_browse:!0,allowed_toolsets:["items","traceability","coverage","variables","domains"],forbidden_tools:[],project_scope:null,require_confirmation_for:[]}}});function Z(){return G}var X=P({"src/middleware/session-policy.ts"(){K(),G=Q}});function ee(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. 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Run 'npx @atoms-tech/atoms-mcp login' to connect your ATOMS account.");if(t.expires_at>Date.now()+6e4){const e=ye(t.access_token);return{access_token:t.access_token,refresh_token:t.refresh_token,user_id:e.sub,email:e.email??t.user_email??""}}process.stderr.write("[atoms-mcp] Refreshing access token...\n");const r=d(me,pe),{data:n,error:i}=await r.auth.refreshSession({refresh_token:t.refresh_token});if(i||!n.session)throw new Error(`Token refresh failed: ${i?.message??"No session returned"}. Re-run 'npx @atoms-tech/atoms-mcp login'.`);const a=n.session;return await oe({access_token:a.access_token,refresh_token:a.refresh_token,expires_at:Date.now()+1e3*(a.expires_in??3600),user_email:a.user?.email}),{access_token:a.access_token,refresh_token:a.refresh_token,user_id:a.user?.id??"",email:a.user?.email??""}}function ye(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,"="),n=JSON.parse(Buffer.from(r,"base64").toString("utf-8"));if(!n.sub)throw new Error("JWT missing 'sub' claim");return n}R(he,{getValidToken:()=>ge});var be,we,ve,je,xe=P({"src/auth/refresh.ts"(){_e(),fe()}});async function Se(){if(be&&je>Date.now()+6e4)return be;be&&process.stderr.write("[atoms-mcp] Token expiring, refreshing client...\n");const{access_token:e,user_id:t,email:r}=await ge(),n=e.split(".");if(3===n.length)try{const e=JSON.parse(Buffer.from(n[1].replace(/-/g,"+").replace(/_/g,"/"),"base64").toString());je=1e3*(e.exp??0)}catch{je=Date.now()+36e5}const i=d(me,pe,{global:{headers:{Authorization:`Bearer ${e}`}}});return we=t,ve=r,be=i}function ke(){if(!we)throw new Error("Not authenticated. Call getClient() first.");return we}async function Ie(e,t){const r=ke(),{data:n,error:i}=await e.from("projects").select("org_id").eq("id",t).maybeSingle();if(i||!n)throw new Error(`Project '${t}' not found`);const{data:a,error:o}=await e.from("org_members").select("role").eq("user_id",r).eq("org_id",n.org_id).maybeSingle();if(o||!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}var Ee,Te,Oe,He,Ce,De=P({"src/db/client.ts"(){xe(),fe(),be=null,we=null,ve=null,je=0}});function Ue(e,t=Te){if("string"!=typeof e)return"";const r=e.replace(He,"").replace(Ce,"");return r.length<=t?r:r.slice(0,t)+"..."}function Pe(e,t){return{status:"success",data:e,...t?{meta:t}:{}}}function Re(e,t,r){return{total_count:e,limit:t,offset:r,has_more:r+t<e}}function qe(e,t){return{status:"error",message:e,next_steps:t}}function Ae(e,t){return qe(`${e} '${Ue(t)}' not found`,[`Verify the ${e.toLowerCase()} ID is correct`,"Use atoms_list_items or atoms_search to find valid IDs"])}function Me(e){return qe(`${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 $e(e){return qe(`Validation error: ${Ue(e,Oe)}`,["Check the parameter types and constraints in the tool description","Ensure all required parameters are provided"])}function Ne(){return qe("Not authenticated. Run 'npx @atoms-tech/atoms-mcp login' first.",["Run: npx @atoms-tech/atoms-mcp login","Or set ATOMS_ACCESS_TOKEN environment variable"])}function Ve(e){return qe("Rate limited: too many requests to ATOMS API.",[e?`Wait ${e} seconds before retrying.`:"Wait a few seconds before retrying.","Reduce the frequency of back-to-back tool calls"])}function We(e){const t=e instanceof Error?e.message:String(e);return/not authenticated/i.test(t)?Ne():/rate.?limit|too many requests|429/i.test(t)?Ve():/invalid input syntax|invalid json|unexpected token|malformed|json parse/i.test(t)?qe(`Parse error: ${Ue(t,Oe)}`,["Check that body/title/summary fields contain valid text (no unexpected control characters)","If the content was generated programmatically, validate the string before passing it","Simplify the content and retry — if it succeeds, the original content has a malformed character"]):Fe(t)}function Fe(e){return/row.level security|permission denied for/i.test(e)?qe("Permission denied: your account does not have write access to this project.",["Verify you have editor or admin role in this project","Contact your org admin to upgrade your permissions","Use atoms_list_projects to confirm the project_id is one you have access to"]):qe(`Database error: ${Ue(e,Oe)}`,["This may be a temporary issue — try again","If the error persists, check that the project_id is valid"])}function Le(e){const t=JSON.stringify(e,null,2);if(t.length>Ee&&"success"===e.status&&Array.isArray(e.data)){const t=Math.max(1,Math.floor(e.data.length/2)),r={...e,data:e.data.slice(0,t),meta:{...e.meta,truncated:!0,truncation_message:`Response truncated from ${e.data.length} to ${t} items. Use 'offset' parameter or add filters to see more results.`}};return{content:[{type:"text",text:JSON.stringify(r,null,2)}],structuredContent:r}}return{content:[{type:"text",text:t}],structuredContent:e}}function Je(e){return{content:[{type:"text",text:JSON.stringify(e,null,2)}],structuredContent:e,isError:!0}}var ze,Be=P({"src/tools/_base.ts"(){Ee=25e3,Te=50,Oe=200,He=new RegExp("[\\u0000-\\u001F\\u007F]","g"),Ce=new RegExp("[\\u200B-\\u200F\\u202A-\\u202E\\u2060-\\u206F\\uFEFF]","g")}});var Qe=P({"src/apps/register.ts"(){ze={resourceDomains:["fonts.googleapis.com","fonts.gstatic.com"]}}});async function Ge(e,t,r){let n=e.from("items").select("*",{count:"exact"}).eq("project_id",t).is("deleted_at",null).order("created_at",{ascending:!0});r.type&&(n=n.eq("type",r.type)),r.domain&&(n=n.filter("data->tags->domains","cs",JSON.stringify([r.domain]))),r.level&&(n=n.filter("data->tags->>level","eq",r.level)),n=n.range(r.offset,r.offset+r.limit-1);const{data:i,error:a,count:o}=await n;if(a)throw new Error(a.message);return{items:i??[],totalCount:o??0}}async function Ye(e,t,r){const{data:n,error:i}=await e.from("items").select("*").eq("id",r).eq("project_id",t).is("deleted_at",null).maybeSingle();if(i)throw new Error(i.message);return n}async function Ke(e,t,r,n){const i=r.trim();if(!i)return{items:[],totalCount:0};let a=e.from("items").select("*",{count:"exact"}).eq("project_id",t).is("deleted_at",null).or(`title.ilike.%${i}%,data->>body.ilike.%${i}%,data->>summary.ilike.%${i}%`).limit(n.limit);n.type&&(a=a.eq("type",n.type));const{data:o,error:s,count:d}=await a;if(s)throw new Error(s.message);return{items:o??[],totalCount:d??0}}async function Ze(e,t,r){const n="requirement"===r?"REQ":"test-case"===r?"TC":"note"===r?"NOTE":"TABLE",{data:i,error:a}=await e.rpc("next_item_id",{p_project_id:t,p_prefix:n});if(a)throw new Error(`ID generation failed: ${a.message}`);return i}var Xe=P({"src/db/queries.ts"(){}}),et={};async function tt(){try{const e=await Se(),t=await async function(e){const{data:t,error:r}=await e.from("projects").select("id, name, description, org_id, created_at, organizations(name)").is("deleted_at",null).order("created_at",{ascending:!1});if(r)throw new Error(r.message);return(t??[]).map(e=>({id:e.id,name:e.name,description:e.description,org_id:e.org_id,org_name:e.organizations?.name??"Unknown",created_at:e.created_at}))}(e),r=B(),n=Z().project_scope,i=n?new Set(n):null;return Le(Pe(t.filter(e=>!r||e.id===r).filter(e=>!i||i.has(e.id)).map(e=>({id:e.id,name:e.name,description:e.description,org_id:e.org_id,org_name:e.org_name,created_at:e.created_at}))))}catch(e){return Je(Fe(e instanceof Error?e.message:"Unknown error"))}}R(et,{listProjectsHandler:()=>tt});var rt=P({"src/tools/list-projects.ts"(){De(),Xe(),Y(),X(),Be()}}),nt={};async function it(e){try{const t=await Se(),{items:r,totalCount:n}=await Ge(t,e.project_id,{type:e.type,domain:e.domain,level:e.level,limit:e.limit,offset:e.offset});return Le(Pe(r.map(e=>({id:e.id,title:e.title,type:e.type,status:e.data?.status,domains:e.data?.tags?.domains??[],level:e.data?.tags?.level})),Re(n,e.limit,e.offset)))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(nt,{listItemsHandler:()=>it});var at=P({"src/tools/list-items.ts"(){De(),Xe(),Be()}}),ot={};async function st(e){try{const t=await Se(),r=await Ye(t,e.project_id,e.item_id);if(!r)return Je(Ae("Item",e.item_id));const n=await async function(e,t,r){const{data:n,error:i}=await e.from("item_relationships").select("from_id, to_id, type").eq("project_id",t).or(`from_id.eq.${r},to_id.eq.${r}`);if(i)throw new Error(i.message);return n??[]}(t,e.project_id,e.item_id),i={parents:[],children:[],related:[],verified_by:[],verifies:[]};for(const t of n)if(t.from_id===e.item_id)t.type in i&&i[t.type].push(t.to_id);else{const e={parent:"children",child:"parents",verified_by:"verifies",verifies:"verified_by",related:"related"}[t.type]??t.type;e in i&&i[e].push(t.from_id)}let a=[];if("test-case"===r.type){const{data:r,error:n}=await t.from("test_results").select("result, run_by, run_at, note").eq("item_id",e.item_id).eq("project_id",e.project_id).order("run_at",{ascending:!1}).limit(20);!n&&r&&(a=r)}return Le(Pe({id:r.id,type:r.type,title:r.title,summary:r.data?.summary,body:r.data?.body,tags:r.data?.tags??{domains:[]},ownership:r.data?.ownership??{primary:null,additional:[]},relationships:i,links:r.data?.links??[],status:r.data?.status,..."test-case"===r.type?{latest_result:a[0]?.result??"not-run",test_results:a}:{},metadata:{created_at:r.created_at,created_by:r.created_by,updated_at:r.updated_at,updated_by:r.updated_by,source_id:r.data?.metadata?.source_id}}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(ot,{getItemHandler:()=>st});var dt=P({"src/tools/get-item.ts"(){De(),Xe(),Be()}}),ct={};async function lt(e){try{const t=await Se(),{items:r,totalCount:n}=await Ke(t,e.project_id,e.query,{type:e.type,limit:e.limit});return Le(Pe(r.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})),Re(n,e.limit,0)))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(ct,{searchHandler:()=>lt});var mt=P({"src/tools/search.ts"(){De(),Xe(),Be()}}),pt={};async function ut(e){try{const t=await Se(),{covered:r,uncovered:n,total:i}=await async function(e,t,r){const{data:n,error:i}=await e.from("items").select("*").eq("project_id",t).eq("type","requirement").is("deleted_at",null);if(i)throw new Error(i.message);const a=(n??[]).filter(e=>!(r.domain&&!(e.data?.tags?.domains??[]).includes(r.domain)||r.level&&e.data?.tags?.level!==r.level)),{data:o,error:s}=await e.from("item_relationships").select("from_id").eq("project_id",t).eq("type","verified_by");if(s)throw new Error(s.message);const d=new Set((o??[]).map(e=>e.from_id));return{covered:a.filter(e=>d.has(e.id)),uncovered:a.filter(e=>!d.has(e.id)),total:a.length}}(t,e.project_id,{domain:e.domain,level:e.level}),a=n.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}));return Le(Pe({covered:r.length,uncovered:n.length,total:i,coverage_percent:i>0?Math.round(r.length/i*1e3)/10:100,uncovered_items:a}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(pt,{getCoverageHandler:()=>ut});var _t=P({"src/tools/get-coverage.ts"(){De(),Xe(),Be()}}),ft={};async function ht(e){try{const t=await Se(),r=await async function(e,t,r,n){const{data:i,error:a}=await e.from("change_history").select("*").eq("item_id",r).eq("project_id",t).order("changed_at",{ascending:!1}).limit(n);if(a)throw new Error(a.message);return i??[]}(t,e.project_id,e.item_id,e.limit),n=r.map(e=>{const t=[],r=e.old_data,n=e.new_data;if(r&&n){const e=new Set([...Object.keys(r),...Object.keys(n)]);for(const i of e)JSON.stringify(r[i])!==JSON.stringify(n[i])&&t.push(i)}else n?t.push("(created)"):r&&t.push("(deleted)");return{id:e.id,event_type:e.event_type,changed_by:e.changed_by??null,changed_at:e.changed_at,actor:e.actor??"user",session_id:e.session_id??null,fields_changed:t}});return Le(Pe(n,Re(n.length,e.limit,0)))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(ft,{getHistoryHandler:()=>ht});var gt=P({"src/tools/get-history.ts"(){De(),Xe(),Be()}}),yt={};async function bt(e){try{const t=await Se(),{data:r,error:n}=await t.from("items").select("id, title, type, data").eq("project_id",e.project_id).is("deleted_at",null);if(n)throw new Error(n.message);if(!r||0===r.length)return Le(Pe({mermaid:"graph TD\n empty[No items in project]"}));const{data:i,error:a}=await t.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(a)throw new Error(a.message);const o=new Map;for(const e of r)o.set(e.id,e);const s=["graph TD"],d=new Set,c=new Set,l=(new Set((i??[]).filter(e=>"child"===e.type).map(e=>e.to_id)),new Set((i??[]).filter(e=>"parent"===e.type).map(e=>e.from_id)));let m;m=e.root_item_id?[e.root_item_id]:r.filter(e=>!l.has(e.id)).filter(t=>!(!e.include_tests&&"test-case"===t.type)).map(e=>e.id);const p=m.map(e=>({id:e,depth:0}));for(;p.length>0;){const{id:t,depth:r}=p.shift();if(d.has(t)||r>e.depth)continue;d.add(t);const n=o.get(t);if(!n)continue;if(!e.include_tests&&"test-case"===n.type)continue;const a=wt(n.title),l="requirement"===n.type?`["${a}"]`:"test-case"===n.type?`(["${a}"])`:`("${a}")`;s.push(` ${t}${l}`);for(const n of i??[]){if(n.from_id!==t)continue;const i=o.get(n.to_id);if(!i)continue;if(!e.include_tests&&"test-case"===i.type)continue;const a=`${n.from_id}-${n.type}-${n.to_id}`;c.has(a)||(c.add(a),"child"===n.type?s.push(` ${t} --\x3e ${n.to_id}`):"verified_by"===n.type?s.push(` ${t} -.->|verified_by| ${n.to_id}`):"related"===n.type&&s.push(` ${t} -.- ${n.to_id}`),!d.has(n.to_id)&&r+1<=e.depth&&p.push({id:n.to_id,depth:r+1}))}}return Le(Pe({mermaid:s.join("\n"),node_count:d.size,edge_count:c.size}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}function wt(e){return e.replace(/"/g,"'").replace(/[[\]{}()]/g,"").substring(0,50)}R(yt,{exportMermaidHandler:()=>bt});var vt=P({"src/tools/export-mermaid.ts"(){De(),Be()}}),jt={};async function xt(e){try{const t=await Se(),r=ke();try{await Ie(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Je(Me("Viewer"));throw e}if(e.domains&&e.domains.length>0){const{data:r}=await t.from("metadata").select("domains").eq("project_id",e.project_id).maybeSingle(),n=r?.domains??[];if(n.length>0){const t=e.domains.filter(e=>!n.includes(e));if(t.length>0)return Je($e(`Unknown domain${t.length>1?"s":""}: ${t.join(", ")}. 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t.from("change_history").insert({item_id:n,project_id:e.project_id,changed_by:r,event_type:"created",old_data:null,new_data:a,actor:"mcp_claude",session_id:$r()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),!1===e.echo?Le(Pe({id:n,type:e.type})):Le(Pe({id:n,type:e.type,title:e.title,summary:e.summary??"",body:e.body??"",domains:e.domains??[],level:e.level??"",project_id:e.project_id}))}catch(e){return Je(We(e))}}R(jt,{createItemHandler:()=>xt});var St=P({"src/tools/create-item.ts"(){De(),Xe(),Wr(),Be()}}),kt={};async function It(e){try{const t=await Se(),r=ke();try{await Ie(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Je(Me("Viewer"));throw e}const n=async(n,i,a,o)=>{const s=await Ye(t,e.project_id,n);if(!s)return{updated_fields:[],error:`Item "${n}" not found`};if(void 0!==i.domains&&i.domains.length>0){const{data:r}=await t.from("metadata").select("domains").eq("project_id",e.project_id).maybeSingle(),n=r?.domains??[];if(n.length>0){const e=i.domains.filter(e=>!n.includes(e));if(e.length>0)return{updated_fields:[],error:`Unknown domains: ${e.join(", ")}`}}}const d={...s.data},c={...s.data},l=[];void 0!==i.title&&(c.title=i.title,l.push("title")),void 0!==i.body&&(c.body=i.body,l.push("body")),void 0!==i.summary&&(c.summary=i.summary,l.push("summary")),void 0!==i.domains&&(c.tags={...c.tags,domains:i.domains},l.push("domains")),void 0!==i.level&&(c.tags={...c.tags,level:i.level},l.push("level")),void 0!==i.status&&(c.status=i.status,l.push("status")),c.metadata={...c.metadata,updated_at:(new Date).toISOString(),updated_by:r};const{error:m}=await t.from("items").update({title:i.title??s.title,data:c,updated_by:r}).eq("id",n).eq("project_id",e.project_id);if(m)return{updated_fields:[],error:m.message};const p={item_id:n,project_id:e.project_id,changed_by:r,event_type:"updated",old_data:d,new_data:c,actor:"mcp_claude",session_id:$r()};return a&&(p.batch_id=a),o&&(p.reason=o),await t.from("change_history").insert(p).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),{updated_fields:l,updatedData:c,itemType:s.type}};if(e.updates&&Array.isArray(e.updates)){const t=crypto.randomUUID(),r=!0===e.continue_on_error,i=[],a=[];for(const o of e.updates){const{updated_fields:s,error:d}=await n(o.item_id,o,t,e.reason);if(d){if(!r)return Je($e(`Batch stopped at "${o.item_id}": ${d}. ${i.length} item(s) already updated.`));a.push({item_id:o.item_id,error:d})}else i.push({id:o.item_id,updated_fields:s})}return Le(Pe({batch_id:t,updated:i.length,results:!1===e.echo?void 0:i,errors:a}))}if(!e.item_id)return Je($e("Provide either item_id (single) or updates[] (array form)."));const{updated_fields:i,updatedData:a,itemType:o,error:s}=await n(e.item_id,{title:e.title,body:e.body,summary:e.summary,domains:e.domains,level:e.level,status:e.status},void 0,e.reason);if(s)return s.includes("not found")?Je(Ae("Item",e.item_id)):s.includes("Unknown domain")?Je($e(s)):Je(Fe(s));if(!1===e.echo)return Le(Pe({id:e.item_id,updated_fields:i}));const d=a??{};return Le(Pe({id:e.item_id,type:o,title:d.title??"",summary:d.summary??"",body:d.body??"",domains:d.tags?.domains??[],level:d.tags?.level??"",updated_fields:i}))}catch(e){return Je(We(e))}}R(kt,{updateItemHandler:()=>It});var Et,Tt,Ot=P({"src/tools/update-item.ts"(){De(),Xe(),Wr(),Be()}});function Ht(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!!Z().require_confirmation_for.includes(e)}function Ct(e,t=Et){const 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Le(Pe({status:"confirmation_required",preview:{id:e.item_id,title:n.title,type:n.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 ${r.expires_in_seconds}s to execute.`}))}const r=Dt(e.confirmation_token,t);if(!r.valid)return Je($e(`confirmation_token rejected: ${r.reason}`))}const{error:i}=await t.from("items").update({deleted_at:(new Date).toISOString()}).eq("id",e.item_id).eq("project_id",e.project_id);if(i)throw new Error(i.message);return await t.from("change_history").insert({item_id:e.item_id,project_id:e.project_id,changed_by:r,event_type:"deleted",old_data:n.data,new_data:null,actor:"mcp_claude",session_id:$r()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),Le(Pe({id:e.item_id,title:n.title,type:n.type,deleted:!0,message:`Item ${e.item_id} 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Split into multiple calls.`));const t=await Se(),r=ke();try{await Ie(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Je(Me("Viewer"));throw e}if(Ht("atoms_bulk_import")){const t={tool:"atoms_bulk_import",project_id:e.project_id,target:Pt(e.items)};if(!e.confirmation_token){const r=Ct(t),n={};for(const t of e.items)n[t.type]=(n[t.type]??0)+1;return Le(Pe({status:"confirmation_required",preview:{total_items:e.items.length,by_type:n,sample_titles:e.items.slice(0,5).map(e=>e.title)},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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t.from("items").insert(d);if(l)for(const{itemId:e,input:r,index:n}of s){const i=d.find(t=>t.id===e);if(!i)continue;const{error:s}=await t.from("items").insert(i);s?o.push({index:n,title:r.title,error:s.message}):a.push({id:e,title:r.title,type:r.type})}else for(const{itemId:e,input:t}of s)a.push({id:e,title:t.title,type:t.type});const m=s.filter(({input:e})=>e.parent_id).filter(({itemId:e})=>a.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}));m.length>0&&await t.from("item_relationships").insert(m).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: bulk relationship sync failed: ${e.message}\n`)});const p=a.map(t=>({item_id:t.id,project_id:e.project_id,changed_by:r,event_type:"created",old_data:null,new_data:c.get(t.id)??null,actor:"mcp_claude",session_id:i}));return p.length>0&&await t.from("change_history").insert(p).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: bulk change_history log failed: ${e.message}\n`)}),Le(Pe({created:a.length,items:a,errors:o.length>0?o:[],project_id:e.project_id}))}catch(e){return Je(We(e))}}R(Jt,{bulkImportHandler:()=>zt});var Bt=P({"src/tools/bulk-import.ts"(){De(),Xe(),Wr(),qt(),Be()}}),Qt={};async function Gt(e){try{const t=await Se(),r=ke(),n=ve??"";try{await Ie(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Je(Me("Viewer"));throw e}const i=await Ye(t,e.project_id,e.item_id);if(!i)return Je(Ae("Item",e.item_id));if("test-case"!==i.type)return Je($e(`Item '${e.item_id}' is a ${i.type}, not a test-case`));const a=(new Date).toISOString(),{error:o}=await t.from("test_results").insert({item_id:e.item_id,project_id:e.project_id,result:e.result,run_by:n||r,run_at:a,note:e.note??null});if(o)throw new Error(o.message);return await t.from("change_history").insert({item_id:e.item_id,project_id:e.project_id,changed_by:r,event_type:"test_result_recorded",old_data:null,new_data:{result:e.result,run_at:a,note:e.note},actor:"mcp_claude",session_id:$r()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),Le(Pe({item_id:e.item_id,result:e.result,run_at:a,run_by:n||r,note:e.note??null,message:`Test result '${e.result}' recorded for ${e.item_id}`}))}catch(e){return Je(We(e))}}R(Qt,{recordTestResultHandler:()=>Gt});var Yt,Kt,Zt,Xt,er=P({"src/tools/record-test-result.ts"(){De(),Xe(),Wr(),Be()}}),tr={};async function rr(e){try{const t=Math.min(Math.max(e.depth??5,1),10),r=await Se(),n=await Ye(r,e.project_id,e.item_id);if(!n)return Je(Ae("Item",e.item_id));const{data:i,error:a}=await r.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(a)throw new Error(a.message);const{data:o,error:s}=await r.from("items").select("id, title, type").eq("project_id",e.project_id).is("deleted_at",null);if(s)throw new Error(s.message);const d=new Map;for(const e of o??[])d.set(e.id,{title:e.title,type:e.type});const c=new Map,l=(e,t,r)=>{c.has(e)||c.set(e,[]),c.get(e).push({neighbor:t,relType:r})},m=e.relationship_types?new Set(e.relationship_types):null;for(const t of i??[]){const r=t.type;if(("upstream"===e.direction||"both"===e.direction)&&(Kt.includes(r)&&(m&&!m.has(r)||l(t.from_id,t.to_id,r)),Zt.includes(r))){const e=Xt[r]??r;m&&!m.has(e)||l(t.to_id,t.from_id,e)}if(("downstream"===e.direction||"both"===e.direction)&&(Zt.includes(r)&&(m&&!m.has(r)||l(t.from_id,t.to_id,r)),Kt.includes(r))){const e=Xt[r]??r;m&&!m.has(e)||l(t.to_id,t.from_id,e)}"related"===r&&(m&&!m.has("related")||(l(t.from_id,t.to_id,"related"),l(t.to_id,t.from_id,"related")))}const p=new Set;p.add(e.item_id);const u=[],_=[],f=[],h=c.get(e.item_id)??[];for(const t of h)f.push({id:t.neighbor,depth:1,relType:t.relType,from:e.item_id});for(;f.length>0&&u.length<Yt;){const{id:e,depth:r,relType:n,from:i}=f.shift();if(p.has(e)||r>t)continue;p.add(e);const a=d.get(e);if(a&&(u.push({id:e,title:a.title,type:a.type,relationship:n,depth:r,from:i}),_.push({from:i,to:e,type:n}),r<t)){const t=c.get(e)??[];for(const n of t)p.has(n.neighbor)||f.push({id:n.neighbor,depth:r+1,relType:n.relType,from:e})}}const g=d.get(e.item_id),y=g?{id:e.item_id,title:g.title,type:g.type,relationship:"root",depth:0,from:e.item_id}:{id:e.item_id,title:n.title??e.item_id,type:n.type??"unknown",relationship:"root",depth:0,from:e.item_id};return Le(Pe({root:e.item_id,direction:e.direction,depth_limit:t,items:[y,...u],edges:_,total_count:u.length+1,...u.length>=Yt?{truncated:!0,truncation_message:`Results capped at ${Yt} items. Use a smaller depth or filter by relationship_types.`}:{}}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(tr,{traceHandler:()=>rr});var nr=P({"src/tools/trace.ts"(){De(),Xe(),Be(),Yt=200,Kt=["parent","verifies"],Zt=["child","verified_by"],Xt={parent:"child",child:"parent",verifies:"verified_by",verified_by:"verifies",related:"related"}}}),ir={};async function ar(e){try{const t=await Se(),{data:r,error:n}=await t.from("project_variables").select("*").eq("project_id",e.project_id).order("name");if(n)throw new Error(n.message);return Le(Pe({variables:r||[],total:(r||[]).length}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}async function or(e){try{const t=await Se(),{data:r,error:n}=await t.from("project_variables").select("*").eq("project_id",e.project_id).eq("name",e.variable_name).maybeSingle();if(n)throw new Error(n.message);if(!r)return Je(Ae("Variable",e.variable_name));const{data:i}=await t.from("items").select("id, title, type").eq("project_id",e.project_id).is("deleted_at",null),a=`{${e.variable_name}}`,o=(i||[]).filter(e=>(e.data?.body||"").includes(a));return Le(Pe({variable:r,referenced_by:o.map(e=>({id:e.id,title:e.title,type:e.type})),reference_count:o.length}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}async function sr(e){try{const t=await Se(),r=ke();try{await Ie(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Je(Me("Viewer"));throw e}if(!(await t.from("project_variables").select("*").eq("project_id",e.project_id).eq("name",e.variable_name).maybeSingle()).data)return Je(Ae("Variable",e.variable_name));const n={updated_by:r,updated_at:(new Date).toISOString()};void 0!==e.value&&(n.value=e.value),void 0!==e.unit&&(n.unit=e.unit||null),void 0!==e.description&&(n.description=e.description||null);const{data:i,error:a}=await t.from("project_variables").update(n).eq("project_id",e.project_id).eq("name",e.variable_name).select().single();if(a)throw new Error(a.message);return Le(Pe({variable:i}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}async function dr(e){try{const t=await Se(),r=ke();try{await Ie(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Je(Me("Viewer"));throw e}const n=/^[a-zA-Z_][a-zA-Z0-9_]*$/;if(e.variables&&Array.isArray(e.variables)){const i=e.variables.filter(e=>!n.test(e.name));if(i.length>0)return Je($e(`Invalid variable name(s): ${i.map(e=>e.name).join(", ")}. Use letters, digits, underscores; must start with letter or underscore.`));const a=e.variables.map(e=>e.name),o=a.filter((e,t)=>a.indexOf(e)!==t);if(o.length>0)return Je($e(`Duplicate names in batch: ${[...new Set(o)].join(", ")}`));const{data:s}=await t.from("project_variables").select("name").eq("project_id",e.project_id).in("name",a),d=(s??[]).map(e=>e.name);if(d.length>0)return Je($e(`Variable(s) already exist: ${d.join(", ")}. Remove them from the batch or use atoms_update_variable to change values.`));const c=e.variables.map(t=>({project_id:e.project_id,name:t.name,value:t.value,unit:t.unit??null,description:t.description??null,created_by:r,updated_by:r})),{data:l,error:m}=await t.from("project_variables").insert(c).select();if(m)throw new Error(m.message);return Le(Pe({batch_id:crypto.randomUUID(),created:(l??[]).length,variables:!1===e.echo?(l??[]).map(e=>({name:e.name})):l??[],message:`${(l??[]).length} variable(s) created. Reference them as {name} in requirement bodies.`}))}if(!e.name||!e.value)return Je($e("Provide either (name, value) for single variable or variables[] for batch."));if(!n.test(e.name))return Je($e(`Variable name "${e.name}" is invalid. Use letters, digits, and underscores only; must start with a letter or underscore.`));const{data:i,error:a}=await t.from("project_variables").insert({project_id:e.project_id,name:e.name,value:e.value,unit:e.unit??null,description:e.description??null,created_by:r,updated_by:r}).select().single();if(a){if(a.message.includes("unique")||a.message.includes("duplicate"))return Je($e(`Variable "${e.name}" already exists in this project.`));throw new Error(a.message)}return!1===e.echo?Le(Pe({name:e.name})):Le(Pe({variable:i,message:`Variable "${e.name}" created. Reference it in requirement bodies as {${e.name}}.`}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}async function cr(e){try{const t=await Se();try{await Ie(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Je(Me("Viewer"));throw e}const{data:r}=await t.from("project_variables").select("id").eq("project_id",e.project_id).eq("name",e.name).maybeSingle();if(!r)return Je(Ae("Variable",e.name));const{data:n}=await t.from("items").select("id").eq("project_id",e.project_id).is("deleted_at",null).filter("data->>body","ilike",`%{${e.name}}%`),i=(n??[]).length;if(i>0&&!e.force)return Je($e(`Variable "${e.name}" is referenced in ${i} item${i>1?"s":""}. Use force=true to delete anyway, or remove all {${e.name}} references first.`));if(Ht("atoms_delete_variable")){const t={tool:"atoms_delete_variable",project_id:e.project_id,target:e.name};if(!e.confirmation_token){const r=Ct(t);return Le(Pe({status:"confirmation_required",preview:{variable_name:e.name,referenced_by_items:i,would_orphan_references:i>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 ${r.expires_in_seconds}s to execute.`}))}const r=Dt(e.confirmation_token,t);if(!r.valid)return Je($e(`confirmation_token rejected: ${r.reason}`))}const{error:a}=await t.from("project_variables").delete().eq("project_id",e.project_id).eq("name",e.name);if(a)throw new Error(a.message);return Le(Pe({deleted:!0,name:e.name,referenced_by_items:i,warning:i>0?`${i} item${i>1?"s":""} still contain {${e.name}} — those references are now unresolved.`:void 0}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(ir,{createVariableHandler:()=>dr,deleteVariableHandler:()=>cr,getVariableHandler:()=>or,listVariablesHandler:()=>ar,updateVariableHandler:()=>sr});var lr=P({"src/tools/variables.ts"(){De(),qt(),Be()}}),mr={};async function pr(e,t){const{data:r}=await e.from("metadata").select("domains, levels").eq("project_id",t).maybeSingle();return{domains:r?.domains??[],levels:r?.levels??[]}}async function ur(e,t,r,n){const{error:i}=await e.from("metadata").upsert({project_id:t,domains:r,levels:n},{onConflict:"project_id"});if(i)throw new Error(i.message)}async function _r(e){try{const t=await Se(),{domains:r}=await pr(t,e.project_id),{counts:n,orphans:i}=await async function(e,t,r){const{data:n}=await e.from("items").select("data").eq("project_id",t).is("deleted_at",null),i={};for(const e of r)i[e]=0;const a={};for(const e of n??[]){const t=e.data?.tags?.domains??[];for(const e of t)a[e]=(a[e]??0)+1,e in i&&i[e]++}const o=new Set(r),s={};for(const[e,t]of Object.entries(a))o.has(e)||(s[e]=t);return{counts:i,orphans:s}}(t,e.project_id,r),a=r.map(e=>({name:e,registered:!0,item_count:n[e]??0})),o=Object.entries(i).map(([e,t])=>({name:e,registered:!1,item_count:t})).sort((e,t)=>e.name.localeCompare(t.name)),s=[...a,...o];return Le(Pe({domains:s,total:s.length,registered_count:a.length,unregistered_count:o.length,note:o.length>0?`${o.length} unregistered tag(s) found on items. Use atoms_create_domain to register them, or atoms_update_item to remove them.`:void 0}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}async function fr(e){try{const t=await Se();try{await Ie(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Je(Me("Viewer"));throw e}const{domains:r,levels:n}=await pr(t,e.project_id),i=e.name.trim().toLowerCase();return i?r.includes(i)?Je($e(`Domain "${i}" already exists in this project.`)):(await ur(t,e.project_id,[...r,i],n),Le(Pe({domain:{name:i},message:`Domain "${i}" registered. You can now tag items with domains=["${i}"].`}))):Je($e("Domain name cannot be empty."))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}async function hr(e){try{const t=await Se(),r=ke();try{await Ie(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Je(Me("Viewer"));throw e}const{domains:n,levels:i}=await pr(t,e.project_id),a=e.name.trim().toLowerCase(),o=e.new_name.trim().toLowerCase();if(!o)return Je($e("new_name cannot be empty."));const s=n.includes(a);if(!s){const{data:r}=await t.from("items").select("id").eq("project_id",e.project_id).is("deleted_at",null).filter("data->tags->domains","cs",JSON.stringify([a])).limit(1);if(!r||0===r.length)return Je(Ae("Domain",a))}if(o!==a&&n.includes(o))return Je($e(`Domain "${o}" already exists. Choose a different name.`));const{data:d,error:c}=await t.from("items").select("id, data").eq("project_id",e.project_id).is("deleted_at",null).filter("data->tags->domains","cs",JSON.stringify([a]));if(c)throw new Error(c.message);const l=(d??[]).length;if(e.dry_run)return Le(Pe({dry_run:!0,rename:{from:a,to:o},items_affected:l,message:`Dry run: renaming "${a}" → "${o}" would update ${l} item${1!==l?"s":""}. Call again with dry_run=false to apply.`}));let m;return m=s?n.map(e=>e===a?o:e):n.includes(o)?n:[...n,o],await ur(t,e.project_id,m,i),(new Date).toISOString(),await Promise.all((d??[]).map(n=>{const i=(n.data?.tags?.domains??[]).map(e=>e===a?o:e),s={...n.data,tags:{...n.data?.tags??{},domains:i}};return t.from("items").update({data:s,updated_by:r}).eq("id",n.id).eq("project_id",e.project_id)})),Le(Pe({domain:{name:o},renamed_from:a,items_updated:l,message:`Domain renamed "${a}" → "${o}". ${l} item${1!==l?"s":""} updated.`}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}async function gr(e){try{const t=await Se(),r=ke();try{await Ie(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return Je(Me("Viewer"));throw e}const{domains:n,levels:i}=await pr(t,e.project_id),a=e.name.trim().toLowerCase(),o=n.includes(a),{data:s,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=(s??[]).length;if(!o&&0===c)return Je(Ae("Domain",a));if(c>0&&!e.force)return Je($e(`Domain "${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(Ht("atoms_delete_domain")){const t={tool:"atoms_delete_domain",project_id:e.project_id,target:a};if(!e.confirmation_token){const e=Ct(t);return Le(Pe({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 ${e.expires_in_seconds}s to execute.`}))}const r=Dt(e.confirmation_token,t);if(!r.valid)return Je($e(`confirmation_token rejected: ${r.reason}`))}const l=o?n.filter(e=>e!==a):n;return await ur(t,e.project_id,l,i),(new Date).toISOString(),c>0&&await Promise.all((s??[]).map(n=>{const i={...n.data,tags:{...n.data?.tags??{},domains:(n.data?.tags?.domains??[]).filter(e=>e!==a)}};return t.from("items").update({data:i,updated_by:r}).eq("id",n.id).eq("project_id",e.project_id)})),Le(Pe({deleted:!0,name:a,items_updated:c,message:c>0?`Domain "${a}" deleted and stripped from ${c} item${c>1?"s":""}.`:`Domain "${a}" deleted.`}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(mr,{createDomainHandler:()=>fr,deleteDomainHandler:()=>gr,listDomainsHandler:()=>_r,updateDomainHandler:()=>hr});var yr=P({"src/tools/domains.ts"(){De(),qt(),Be()}}),br={};async function wr(e){try{const t=await Se(),{data:r,error:n}=await t.from("projects").select("id, name").eq("id",e.project_id).is("deleted_at",null).maybeSingle();if(n)throw new Error(n.message);if(!r)return Je(Ae("Project",e.project_id));const{data:i,error:a}=await t.from("items").select("id, type, data").eq("project_id",e.project_id).is("deleted_at",null);if(a)throw new Error(a.message);const o=i??[],s={requirements:0,test_cases:0,notes:0},d=[],c=[];for(const e of o)if("requirement"===e.type){s.requirements++;const t=e.data?.tags?.domains??[];c.push({id:e.id,domains:t})}else"test-case"===e.type?(s.test_cases++,d.push(e.id)):"note"===e.type&&s.notes++;const l={passed:0,failed:0,blocked:0,not_run:0};if(d.length>0){const{data:r,error:n}=await t.from("test_results").select("item_id, result, run_at").eq("project_id",e.project_id).order("run_at",{ascending:!1});if(n)throw new Error(n.message);const i=new Map;for(const e of r??[])i.has(e.item_id)||i.set(e.item_id,e.result);for(const e of d){const t=i.get(e);t&&"not-run"!==t?"passed"===t?l.passed++:"failed"===t?l.failed++:"blocked"===t?l.blocked++:l.not_run++:l.not_run++}}const{data:m,error:p}=await t.from("item_relationships").select("from_id").eq("project_id",e.project_id).eq("type","verified_by");if(p)throw new Error(p.message);const u=new Set((m??[]).map(e=>e.from_id)),_=c.filter(e=>u.has(e.id)).length,f=c.length,h={covered:_,uncovered:f-_,total:f,percent:f>0?Math.round(_/f*1e3)/10:100},g=new Map;for(const e of c){const t=e.domains.length>0?e.domains:["(untagged)"],r=u.has(e.id);for(const e of t){g.has(e)||g.set(e,{covered:0,total:0});const t=g.get(e);t.total++,r&&t.covered++}}const y=Array.from(g.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})),b=new Date;b.setDate(b.getDate()-7);const{count:w,error:v}=await t.from("change_history").select("id",{count:"exact",head:!0}).eq("project_id",e.project_id).gte("changed_at",b.toISOString());if(v)throw new Error(v.message);return Le(Pe({project_id:e.project_id,project_name:r.name,counts:s,test_status:l,coverage:h,coverage_by_domain:y,recent_changes:w??0,last_updated:(new Date).toISOString()}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(br,{projectSummaryHandler:()=>wr});var vr,jr=P({"src/tools/project-summary.ts"(){De(),Be()}}),xr={};async function Sr(e){try{const t=await Se();let r,n;if(e.query&&e.query.trim().length>0){const i=await Ke(t,e.project_id,e.query,{type:e.type,limit:e.limit});r=i.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})),n=i.totalCount}else{const i=await Ge(t,e.project_id,{type:e.type,domain:e.domain,level:e.level,limit:e.limit,offset:e.offset});r=i.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})),n=i.totalCount}const i=await async function(e,t){const{data:r,error:n}=await e.from("items").select("data").eq("project_id",t).is("deleted_at",null);if(n)throw new Error(n.message);const i=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)i.add(t);const r=t.level;r&&a.add(r)}}return{domains:[...i].sort(),levels:[...a].sort()}}(t,e.project_id);return Le(Pe({items:r,filters:{domains:i.domains,levels:i.levels,types:vr},project_id:e.project_id},Re(n,e.limit,e.offset)))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(xr,{browseHandler:()=>Sr});var kr,Ir,Er,Tr,Or=P({"src/tools/browse.ts"(){De(),Xe(),Be(),vr=["requirement","test-case","note","table"]}}),Hr={};async function Cr(e){try{const t=e.direction??"downstream",r=null!=e.depth?Math.min(Math.max(e.depth,1),20):null,n=await Se(),i=await Ye(n,e.project_id,e.item_id);if(!i)return Je(Ae("Item",e.item_id));const{data:a,error:o}=await n.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(o)throw new Error(o.message);const{data:s,error:d}=await n.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 s??[])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||(Ir.includes(r)&&m(e.from_id,e.to_id,r),Er.includes(r)&&m(e.to_id,e.from_id,Tr[r]??r)),"downstream"!==t&&"both"!==t||(Er.includes(r)&&m(e.from_id,e.to_id,r),Ir.includes(r)&&m(e.to_id,e.from_id,Tr[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<kr;){const{id:e,depth:t,path:n}=f.shift();if(p.has(e))continue;if(null!==r&&t>r)continue;p.add(e);const i=c.get(e);if(i&&(u.push({item_id:e,title:i.title,type:i.type,depth:t,relationship_path:n}),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:[...n,{from_id:e,to_id:r.neighbor,relationship_type:r.relType}]})}let h=0;if(e.include_variable_refs){const{data:t}=await n.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 n.from("project_variables").select("id, name").in("id",r),i=new Map((t??[]).map(e=>[e.id,e.name])),{data:a}=await n.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>=kr)break;p.add(r);const n=c.get(r);if(!n)continue;const a=i.get(t.variable_id)??t.variable_id;u.push({item_id:r,title:n.title,type:n.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 Le(Pe({root:{item_id:e.item_id,title:y?.title??i.title,type:y?.type??i.type},impacted_items:u,summary:{total_impacted:u.length,by_type:g,max_depth_reached:_,...h>0?{variable_impact_count:h}:{},...u.length>=kr?{truncated:!0}:{}}}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?Je(Ne()):Je(Fe(e instanceof Error?e.message:String(e)))}}R(Hr,{impactAnalysisHandler:()=>Cr});var Dr,Ur,Pr,Rr,qr=P({"src/tools/impact-analysis.ts"(){De(),Xe(),Be(),kr=200,Ir=["parent","verifies","traces_to","allocated_from","decomposed_from"],Er=["child","verified_by","allocated_to","decomposes_to","traced_by"],Tr={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"}}});function Ar(t){W(t.toolName)&&function(t,r){const n=`ui://${r.toolName}/${r.htmlFile}`,i=function(e,t){const r=u(import.meta.url),n=o.dirname(r);return o.resolve(n,"apps","src","apps",e,t)}(r.appName,r.htmlFile),a=[...ze.resourceDomains,...r.extraResourceDomains??[]];c(t,r.toolName,{title:r.title,description:r.description,inputSchema:r.inputSchema,annotations:r.annotations,_meta:{ui:{resourceUri:n}}},r.handler),l(t,`${r.title} UI`,n,{mimeType:m},async()=>{const t=await e.readFile(i,"utf-8");return{contents:[{uri:n,mimeType:m,text:t,_meta:{ui:{csp:{resourceDomains:a}}}}]}})}(Dr,t)}function Mr(e,t){return async r=>{const n=function(e,t){if(k.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&&I.has(t))return{allowed:!1,reason:"read_only"};if(e.block_destructive&&E.has(t))return{allowed:!1,reason:"block_destructive"};if(e.block_bulk_import&&T.has(t))return{allowed:!1,reason:"block_bulk_import"};const r=M(t);return void 0===r||e.allowed_toolsets.includes(r)?{allowed:!0}:{allowed:!1,reason:"toolset_disabled"}}(Z(),e);if(!n.allowed)return Je(qe(`Tool ${e} is blocked by org policy.`,[ee(n.reason),"Contact your org admin to adjust the MCP access policy."]));try{!function(e){const t=B();if(!t)return;if("object"!=typeof e||null===e)return;const r=e.project_id;if("string"==typeof r&&r!==t)throw new J(t,r)}(r)}catch(e){if(e instanceof J)return Je(qe("Tool call rejected: project_id is outside the configured ATOMS_MCP_PROJECT_ID scope.",[`This MCP session is bound to project ${e.expectedProjectId}`,"Pass that project_id, or restart without ATOMS_MCP_PROJECT_ID to access other projects"]));throw e}{const e=Z(),t=r?.project_id;if(null!==e.project_scope&&"string"==typeof t&&!e.project_scope.includes(t))return Je(qe("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 i;try{await Se(),i=ke()}catch{return t(r)}const a=function(e){const t=parseInt(process.env.ATOMS_RATE_LIMIT_RPM??"",10)||j,r=Date.now(),n=r-x;let i=S.get(e);if(i||(i={timestamps:[]},S.set(e,i)),i.timestamps=i.timestamps.filter(e=>e>n),i.timestamps.length>=t){const e=i.timestamps[0]+x-r;return{allowed:!1,retryAfterSeconds:Math.ceil(e/1e3)}}return i.timestamps.push(r),{allowed:!0}}(i);if(!a.allowed)return Je(Ve(a.retryAfterSeconds));const o=function(){const e=performance.now();return()=>Math.round(performance.now()-e)}();let s,d="success";try{const e=await t(r),n=e;if(!0===n?.isError){d="error";const e=n?.content;if(e?.[0]?.text)try{s=JSON.parse(e[0].text).message}catch{}}return e}catch(e){throw d="error",s=e instanceof Error?e.message:String(e),e}finally{const t={tool_name:e,params:r,status:d,duration_ms:o(),error_msg:s,project_id:r.project_id,session_id:Pr,client_name:Rr};try{!function(e,t,r){const n={...r.params};delete n.access_token,delete n.refresh_token,delete n.password,e.from("mcp_audit_log").insert({user_id:t,tool_name:r.tool_name,params:n,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 Se(),i,t)}catch{}}}}function $r(){return Pr}var Nr,Vr,Wr=P({"src/server.ts"(){q(),A(),z(),Y(),X(),ne(),De(),Be(),Qe(),Dr=new y({name:"atoms-mcp-server",version:"0.5.0"}),Ur=(e,t,r)=>{if(W(e))return Dr.registerTool(e,t,r)},Pr=f(),Rr=process.env.ATOMS_CLIENT_NAME??"unknown",Ur("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(()=>(_e(),ie)),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(()=>(xe(),he)),{email:t}=await e();return{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)}]}}}),Ur("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}},Mr("atoms_list_projects",async()=>{const{listProjectsHandler:e}=await Promise.resolve().then(()=>(rt(),et));return e()})),Ur("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:b.string().uuid("Must be a valid project UUID").describe("UUID of the project"),type:b.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),domain:b.string().max(64).optional().describe("Filter by domain tag (e.g., 'Safety', 'Performance')"),level:b.string().max(32).optional().describe("Filter by level (System, Subsystem, Component)"),limit:b.number().int().min(1).max(200).default(50).describe("Max results (default 50, max 200)"),offset:b.number().int().min(0).default(0).describe("Pagination offset (default 0)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_list_items",async e=>{const{listItemsHandler:t}=await Promise.resolve().then(()=>(at(),nt));return t(e)})),Ur("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:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Item ID (e.g., REQ-001)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_get_item",async e=>{const{getItemHandler:t}=await Promise.resolve().then(()=>(dt(),ot));return t(e)})),Ur("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 - 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")',inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),query:b.string().min(1).max(1e3).describe("Search text"),type:b.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),limit:b.number().int().min(1).max(100).default(25).describe("Max results (default 25, max 100)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_search",async e=>{const{searchHandler:t}=await Promise.resolve().then(()=>(mt(),ct));return t(e)})),Ar({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\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")',inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),domain:b.string().max(64).optional().describe("Filter by domain tag"),level:b.string().max(32).optional().describe("Filter by level")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Mr("atoms_get_coverage",async e=>{const{getCoverageHandler:t}=await Promise.resolve().then(()=>(_t(),pt));return t(e)})}),Ur("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_claude) 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:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Item ID"),limit:b.number().int().min(1).max(100).default(20).describe("Max entries (default 20)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_get_history",async e=>{const{getHistoryHandler:t}=await Promise.resolve().then(()=>(gt(),ft));return t(e)})),Ar({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\nReturns:\n Mermaid graph string.",inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),root_item_id:b.string().max(20).optional().describe("Root item ID to start from"),depth:b.number().int().min(1).max(10).default(3).describe("Max depth"),include_tests:b.boolean().default(!0).describe("Include test case links")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},extraResourceDomains:["cdn.jsdelivr.net","mermaid.ink"],handler:Mr("atoms_export_mermaid",async e=>{const{exportMermaidHandler:t}=await Promise.resolve().then(()=>(vt(),yt));return t(e)})}),Ur("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\nReturns:\n Created item with generated ID (e.g., \"REQ-058\")\n\nSide effects:\n - Logs to change_history with actor='mcp_claude'\n - Creates relationships if parent_ids provided",inputSchema:{project_id:b.string().uuid().describe("UUID of the target project"),type:b.enum(["requirement","test-case","note"]).describe("Item type"),title:b.string().min(1).max(500).describe("Item title"),body:b.string().max(5e4).optional().describe("Rich text body"),summary:b.string().max(2e3).optional().describe("Brief summary"),domains:b.array(b.string().max(64)).max(20).optional().describe("Domain tags"),level:b.string().max(32).optional().describe("System|Subsystem|Component"),parent_ids:b.array(b.string().max(20)).max(50).optional().describe("Parent item IDs to link"),echo:b.boolean().optional().describe("false → lean {id,type} response, saves ~580 tokens")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Mr("atoms_create_item",async e=>{const{createItemHandler:t}=await Promise.resolve().then(()=>(St(),jt));return t(e)})),Ur("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\nReturns:\n Updated item.",inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).optional().describe("Item ID (single form)"),title:b.string().min(1).max(500).optional().describe("New title"),body:b.string().max(5e4).optional().describe("New body"),summary:b.string().max(2e3).optional().describe("New summary"),domains:b.array(b.string().max(64)).max(20).optional().describe("New domain tags"),level:b.string().max(32).optional().describe("New level"),status:b.enum(["passed","failed","blocked","not-run"]).optional().describe("Test case status"),echo:b.boolean().optional().describe("false → lean {id,updated_fields} response, saves ~580 tokens"),reason:b.string().max(500).optional().describe("Change rationale, persisted in audit history"),updates:b.array(b.object({item_id:b.string().min(1).max(20),title:b.string().min(1).max(500).optional(),body:b.string().max(5e4).optional(),summary:b.string().max(2e3).optional(),domains:b.array(b.string().max(64)).max(20).optional(),level:b.string().max(32).optional(),status:b.enum(["passed","failed","blocked","not-run"]).optional()})).optional().describe("Array form: update many items in one call"),idempotency_key:b.string().max(128).optional().describe("Safe retry key (24h TTL)"),continue_on_error:b.boolean().optional().describe("Allow partial success (default false = atomic)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_update_item",async e=>{const{updateItemHandler:t}=await Promise.resolve().then(()=>(Ot(),kt));return t(e)})),Ur("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:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Item ID to soft-delete"),confirmation_token:b.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}},Mr("atoms_delete_item",async e=>{const{deleteItemHandler:t}=await Promise.resolve().then(()=>(Vt(),At));return t(e)})),Ur("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\nReturns:\n Updated relationship state for both items.",inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),from_id:b.string().min(1).max(20).optional().describe("Source item ID (single form)"),to_id:b.string().min(1).max(20).optional().describe("Target item ID (single form)"),type:b.enum(["parent","child","related","verifies","verified_by"]).optional().describe("Relationship type"),action:b.enum(["add","remove"]).optional().describe("Add or remove"),echo:b.boolean().optional().describe("false → lean response"),reason:b.string().max(500).optional().describe("Change rationale, persisted in audit history"),operations:b.array(b.object({action:b.enum(["add","remove"]),from_id:b.string().min(1).max(20),to_id:b.string().min(1).max(20),type:b.enum(["parent","child","related","verifies","verified_by"])})).optional().describe("Array form: batch relationship ops. Always atomic with DAG cycle detection."),idempotency_key:b.string().max(128).optional().describe("Safe retry key (24h TTL)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_link_items",async e=>{const{linkItemsHandler:t}=await Promise.resolve().then(()=>(Lt(),Wt));return t(e)})),Ar({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_claude' for each created item\n - Creates parent relationships for items with parent_id",inputSchema:{project_id:b.string().uuid().describe("UUID of the target project"),items:b.array(b.object({type:b.enum(["requirement","test-case","note"]).describe("Item type"),title:b.string().min(1).max(500).describe("Item title"),body:b.string().max(5e4).optional().describe("Rich text body"),summary:b.string().max(2e3).optional().describe("Brief summary"),domains:b.array(b.string().max(64)).max(20).optional().describe("Domain tags"),level:b.string().max(32).optional().describe("System|Subsystem|Component"),parent_id:b.string().max(20).optional().describe("Parent item ID to link")})).min(1).max(100).describe("Items to create (1-100)"),confirmation_token:b.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:Mr("atoms_bulk_import",async e=>{const{bulkImportHandler:t}=await Promise.resolve().then(()=>(Bt(),Jt));return t(e)})}),Ur("atoms_record_test_result",{title:"Record Test Result",description:"Record a pass/fail/blocked result for a test case.\n\nAppends to the test results history. 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\nReturns:\n Recorded result with timestamp.\n\nSide effects:\n - Appends to test_results table\n - Logs to change_history with actor='mcp_claude'",inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Test case ID (e.g., TC-001)"),result:b.enum(["passed","failed","blocked","not-run"]).describe("Test result"),note:b.string().max(1e3).optional().describe("Reason or comment for this result")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Mr("atoms_record_test_result",async e=>{const{recordTestResultHandler:t}=await Promise.resolve().then(()=>(er(),Qt));return t(e)})),Ar({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)\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:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Starting item ID"),direction:b.enum(["upstream","downstream","both"]).describe("Traversal direction"),depth:b.number().int().min(1).max(10).default(5).describe("Max traversal depth (default 5)"),relationship_types:b.array(b.enum(["parent","child","related","verifies","verified_by"])).optional().describe("Filter to specific relationship types")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Mr("atoms_trace",async e=>{const{traceHandler:t}=await Promise.resolve().then(()=>(nr(),tr));return t(e)})}),Ur("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\nReturns:\n { variables: [{ id, name, value, unit, description }], total }",inputSchema:{project_id:b.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_list_variables",async e=>{const{listVariablesHandler:t}=await Promise.resolve().then(()=>(lr(),ir));return t(e)})),Ur("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\nReturns:\n { variable, referenced_by: [{ id, title, type }], reference_count }',inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),variable_name:b.string().min(1).max(64).describe("Variable name")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_get_variable",async e=>{const{getVariableHandler:t}=await Promise.resolve().then(()=>(lr(),ir));return t(e)})),Ur("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:b.string().uuid().describe("UUID of the project"),variable_name:b.string().min(1).max(64).describe("Variable name"),value:b.string().max(500).optional().describe("New value"),unit:b.string().max(32).optional().describe("Unit abbreviation"),description:b.string().max(2e3).optional().describe("Description")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_update_variable",async e=>{const{updateVariableHandler:t}=await Promise.resolve().then(()=>(lr(),ir));return t(e)})),Ur("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:b.string().uuid().describe("UUID of the project"),name:b.string().min(1).max(64).optional().describe("Variable name (single form)"),value:b.string().min(1).max(500).optional().describe("Initial value (single form)"),unit:b.string().max(32).optional().describe("Unit abbreviation"),description:b.string().max(2e3).optional().describe("Description"),echo:b.boolean().optional().describe("false → lean response (default true)"),variables:b.array(b.object({name:b.string().min(1).max(64).describe("Variable name"),value:b.string().min(1).max(500).describe("Initial value"),unit:b.string().max(32).optional().describe("Unit abbreviation"),description:b.string().max(2e3).optional().describe("Description")})).optional().describe("Array form: batch variable creation. Atomic — all or none."),idempotency_key:b.string().max(128).optional().describe("Dedup key for retries")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Mr("atoms_create_variable",async e=>{const{createVariableHandler:t}=await Promise.resolve().then(()=>(lr(),ir));return t(e)})),Ur("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:b.string().uuid().describe("UUID of the project"),name:b.string().min(1).max(64).describe("Variable name to delete"),force:b.boolean().optional().describe("Delete even if items reference it (default false)"),confirmation_token:b.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}},Mr("atoms_delete_variable",async e=>{const{deleteVariableHandler:t}=await Promise.resolve().then(()=>(lr(),ir));return t(e)})),Ur("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:b.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_list_domains",async e=>{const{listDomainsHandler:t}=await Promise.resolve().then(()=>(yr(),mr));return t(e)})),Ur("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:b.string().uuid().describe("UUID of the project"),name:b.string().min(1).max(64).describe("Domain name")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Mr("atoms_create_domain",async e=>{const{createDomainHandler:t}=await Promise.resolve().then(()=>(yr(),mr));return t(e)})),Ur("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:b.string().uuid().describe("UUID of the project"),name:b.string().min(1).max(64).describe("Current domain name"),new_name:b.string().min(1).max(64).describe("New domain name"),dry_run:b.boolean().optional().describe("Preview impact without applying (default false)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},Mr("atoms_update_domain",async e=>{const{updateDomainHandler:t}=await Promise.resolve().then(()=>(yr(),mr));return t(e)})),Ur("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:b.string().uuid().describe("UUID of the project"),name:b.string().min(1).max(64).describe("Domain name to delete"),force:b.boolean().optional().describe("Strip from all items and delete (default false)"),confirmation_token:b.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}},Mr("atoms_delete_domain",async e=>{const{deleteDomainHandler:t}=await Promise.resolve().then(()=>(yr(),mr));return t(e)})),Ar({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:b.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Mr("atoms_project_summary",async e=>{const{projectSummaryHandler:t}=await Promise.resolve().then(()=>(jr(),br));return t(e)})}),Ar({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:b.string().uuid().describe("UUID of the project"),type:b.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),domain:b.string().max(64).optional().describe("Filter by domain tag"),level:b.string().max(32).optional().describe("Filter by level (System, Subsystem, Component)"),query:b.string().max(1e3).optional().describe("Full-text search query"),limit:b.number().int().min(1).max(100).default(25).describe("Max results (default 25, max 100)"),offset:b.number().int().min(0).default(0).describe("Pagination offset (default 0)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:Mr("atoms_browse",async e=>{const{browseHandler:t}=await Promise.resolve().then(()=>(Or(),xr));return t(e)})}),Ur("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:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Item ID to analyze (e.g., REQ-001)"),direction:b.enum(["downstream","upstream","both"]).default("downstream").describe("Traversal direction (default: downstream)"),depth:b.number().int().min(1).optional().describe("Max traversal depth. Omit for full depth."),include_variable_refs:b.boolean().default(!0).describe("Reserved for variable-aware impact (future). Default true.")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},Mr("atoms_impact_analysis",async e=>{const{impactAnalysisHandler:t}=await Promise.resolve().then(()=>(qr(),Hr));return t(e)}))}}),Fr={};async function Lr(){const e=h(32).toString("base64url"),t=g("sha256").update(e).digest("base64url"),r=`http://localhost:${Nr}${Vr}`,n=new p(`${ue}/auth/mcp-consent`);return n.searchParams.set("redirect_uri",r),n.searchParams.set("code_challenge",t),n.searchParams.set("code_challenge_method","S256"),new Promise((t,r)=>{let i;function a(){clearTimeout(i)}const o=w(async(n,i)=>{const s=new p(n.url??"/",`http://localhost:${Nr}`);if(s.pathname!==Vr)return i.writeHead(404),void i.end("Not found");try{if("access_denied"===s.searchParams.get("error"))return i.writeHead(200,{"Content-Type":"text/html"}),i.end(zr("Authorization was cancelled.")),a(),o.close(),void r(new Error("Authorization cancelled by user."));const n=s.searchParams.get("code");if(n){const s=await fetch(`${me}/auth/v1/token?grant_type=pkce`,{method:"POST",headers:{"Content-Type":"application/json",apikey:pe},body:JSON.stringify({auth_code:n,code_verifier:e})}),d=await s.json();if(!s.ok||!d.access_token){const e=d.error_description??d.msg??"Unknown error";return i.writeHead(200,{"Content-Type":"text/html"}),i.end(zr(`Code exchange failed: ${e}`)),a(),o.close(),void r(new Error(`Code exchange failed: ${e}`))}let c="authenticated";try{c=JSON.parse(Buffer.from(d.access_token.split(".")[1],"base64").toString()).email??c}catch{}const{createClient:l}=await import("@supabase/supabase-js"),m=l(me,pe,{global:{headers:{Authorization:`Bearer ${d.access_token}`}}}),{data:p,error:u}=await m.from("org_members").select("org_id").limit(1);return u||!p||0===p.length?(i.writeHead(200,{"Content-Type":"text/html"}),i.end(zr('No ATOMS account found for this Google account.<br><br>Please sign up at <a href="https://x.atoms.tech">x.atoms.tech</a> first, then run this login command again.')),a(),o.close(),void r(new Error("No ATOMS account found. Sign up at x.atoms.tech first."))):(await oe({access_token:d.access_token,refresh_token:d.refresh_token,expires_at:Date.now()+1e3*(d.expires_in??3600),user_email:c}),i.writeHead(200,{"Content-Type":"text/html"}),i.end(Jr(c)),a(),o.close(),void t({email:c}))}const d=s.searchParams.get("access_token"),c=s.searchParams.get("refresh_token"),l=parseInt(s.searchParams.get("expires_in")??"3600",10);d&&c?(await oe({access_token:d,refresh_token:c,expires_at:Date.now()+1e3*l}),i.writeHead(200,{"Content-Type":"text/html"}),i.end(Jr("authenticated")),a(),o.close(),t({email:"authenticated"})):(i.writeHead(200,{"Content-Type":"text/html"}),i.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){i.writeHead(500),i.end("Authentication failed"),a(),o.close(),r(e)}});o.on("request",async(e,n)=>{if("POST"===e.method&&"/token"===e.url){let i="";e.on("data",e=>{i+=e.toString()}),e.on("end",async()=>{try{const e=JSON.parse(i);await oe({access_token:e.access_token,refresh_token:e.refresh_token,expires_at:Date.now()+1e3*(e.expires_in??3600),user_email:e.user_email}),n.writeHead(200,{"Content-Type":"application/json"}),n.end(JSON.stringify({ok:!0})),a(),o.close(),t({email:e.user_email??"authenticated"})}catch(e){n.writeHead(500),n.end("Failed to store credentials"),a(),o.close(),r(e)}})}}),o.listen(Nr,"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${n.toString()}\n\n`);try{const{default:e}=await import("open");await e(n.toString())}catch{process.stderr.write("Could not open browser automatically. Please open the URL above.\n")}}),i=setTimeout(()=>{o.close(),r(new Error("Login timed out after 60 seconds. Run 'npx @atoms-tech/atoms-mcp login' to try again."))},6e4)})}function Jr(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 zr(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>`}R(Fr,{login:()=>Lr});var Br=P({"src/auth/login.ts"(){_e(),fe(),Nr=19275,Vr="/callback"}});Wr(),z(),X(),De(),K();var Qr=process.argv.slice(2)[0];(async function(){switch(Qr){case"login":{const{login:e}=await Promise.resolve().then(()=>(Br(),Fr));try{const{email:t}=await e();process.stderr.write(`\n [32m✓[0m Authenticated as ${t}\n`),process.stderr.write(" [32m✓[0m Credentials saved to ~/.atoms/credentials.json\n\n"),process.stderr.write(" [1mNext steps:[0m\n"),process.stderr.write(" [36m$[0m 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(' [90m{\n "mcpServers": {\n "atoms": {\n "command": "npx",\n "args": ["-y", "@atoms-tech/atoms-mcp"]\n }\n }\n }[0m\n\n')}catch(e){process.stderr.write(`\n [31m✗[0m ${e instanceof Error?e.message:String(e)}\n\n`),process.exit(1)}break}case"whoami":{const{getValidToken:e}=await Promise.resolve().then(()=>(xe(),he));try{const{email:t,user_id:r}=await e();process.stderr.write(`\n [32m✓[0m Logged in as ${t}\n [90mUser ID: ${r}[0m\n\n`)}catch(e){process.stderr.write("\n [31m✗[0m Not authenticated.\n Run: npx @atoms-tech/atoms-mcp login\n\n"),process.exit(1)}break}case"logout":{const{clearCredentials:e}=await Promise.resolve().then(()=>(_e(),ie));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 v0.4.0\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");try{const{getValidToken:e}=await Promise.resolve().then(()=>(xe(),he)),{email:t}=await e();process.stderr.write(`[atoms-mcp] Authenticated as ${t}\n`)}catch{process.stderr.write("[atoms-mcp] No credentials found. Starting login flow...\n");try{const{login:e}=await Promise.resolve().then(()=>(Br(),Fr)),{email:t}=await e();process.stderr.write(`[atoms-mcp] Authenticated as ${t}\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`)}}process.stderr.write(`[atoms-mcp] Tool registry: ${function(){const e=V(),t=N(),r=[];r.push(e?"read-only":"read+write"),null===t?r.push("all toolsets"):(r.push(`toolsets=${[...t.allowed].sort().join(",")||"(none — only always-on tools)"}`),t.unknown.length>0&&r.push(`unknown=${t.unknown.join(",")}`));const n=process.env.ATOMS_MCP_PROJECT_ID?.trim();return n&&r.push(`project_scope=${n.slice(0,8)}…`),r.join(" | ")}()}\n`);try{const t=await Se(),r=ke(),n=await async function(e,t){const r=process.env.ATOMS_MCP_ORG_ID?.trim();if(r)return r;const{data:n,error:i}=await e.from("org_members").select("org_id, joined_at").eq("user_id",t).order("joined_at",{ascending:!0}).limit(1).maybeSingle();return i?(process.stderr.write(`[atoms-mcp] Could not resolve session org: ${i.message}\n`),null):n?.org_id??null}(t,r),i=await async function(e,t,r){if(!r)return{role:null,is_member:!1,effective:Q};const{data:n,error:i}=await e.rpc("mcp_resolve_policy",{p_user_id:t,p_org_id:r});return i?(process.stderr.write(`[atoms-mcp] mcp_resolve_policy failed (${i.code}): ${i.message}. Falling back to permissive policy.\n`),{role:null,is_member:!1,effective:Q}):function(e){if(!e||"object"!=typeof e)return{role:null,is_member:!1,effective:Q};const t=e,r="string"==typeof t.role?t.role:null,n=!0===t.is_member,i=t.effective??{},a=(e,t)=>Array.isArray(e)?e.filter(e=>"string"==typeof e):t,o=(e,t)=>"boolean"==typeof e?e:t,s=i.project_scope,d=Array.isArray(s)&&s.length>0?s.filter(e=>"string"==typeof e):null;return{role:r,is_member:n,effective:{read_only:o(i.read_only,Q.read_only),lockdown:o(i.lockdown,Q.lockdown),block_destructive:o(i.block_destructive,Q.block_destructive),block_bulk_import:o(i.block_bulk_import,Q.block_bulk_import),cross_project_browse:o(i.cross_project_browse,Q.cross_project_browse),allowed_toolsets:a(i.allowed_toolsets,Q.allowed_toolsets),forbidden_tools:a(i.forbidden_tools,Q.forbidden_tools),project_scope:d,require_confirmation_for:a(i.require_confirmation_for,Q.require_confirmation_for)}}}(n)}(t,r,n);e={effective:i.effective,role:i.role,org_id:n},G=e.effective,i.is_member&&n?process.stderr.write(`[atoms-mcp] Org policy loaded: org=${n.slice(0,8)}… role=${i.role??"?"} read_only=${i.effective.read_only} lockdown=${i.effective.lockdown}\n`):process.stderr.write("[atoms-mcp] No org membership detected — running with permissive default policy.\n")}catch(e){process.stderr.write(`[atoms-mcp] Could not resolve session policy (${e instanceof Error?e.message:String(e)}). Running with permissive default — RLS still enforces row-level access.\n`)}const t=new v;await Dr.connect(t),process.stderr.write("[atoms-mcp] MCP server running. Waiting for tool calls...\n")}}var e})().catch(e=>{process.stderr.write(`[atoms-mcp] Fatal: ${e instanceof Error?e.message:String(e)}\n`),process.exit(1)});
|
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2
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+
import e,{readFile as t,mkdir as r,writeFile as i,unlink as n}from"fs/promises";import{homedir as a}from"os";import o,{join as s}from"path";import{createClient as d}from"@supabase/supabase-js";import{registerAppTool as c,registerAppResource as l,RESOURCE_MIME_TYPE as m}from"@modelcontextprotocol/ext-apps/server";import{URL as p,fileURLToPath as u}from"url";import _,{randomUUID as f,randomBytes as h,createHash as g}from"crypto";import{McpServer as y}from"@modelcontextprotocol/sdk/server/mcp.js";import{z as b}from"zod";import{createServer as w}from"http";import{StdioServerTransport as v}from"@modelcontextprotocol/sdk/server/stdio.js";var j,x,S=Object.defineProperty,k=Object.getOwnPropertyNames,I=(e,t)=>function(){return e&&(t=(0,e[k(e)[0]])(e=0)),t},E=(e,t)=>{for(var r in t)S(e,r,{get:t[r],enumerable:!0})};function O(e,t=0){if(t>5)return e;if("string"==typeof e){for(const t of x)if(t.test(e.trim()))return"[redacted]";return e}if(Array.isArray(e))return e.map(e=>O(e,t+1));if(null!==e&&"object"==typeof e){const r={};for(const[i,n]of Object.entries(e))j.has(i.toLowerCase())?r[i]="[redacted]":r[i]=O(n,t+1);return r}return e}function T(e){return O(e)}var C,D,H,A,U,q,R,P,M,$=I({"src/middleware/audit.ts"(){j=new Set(["access_token","refresh_token","password","api_key","secret","token","authorization","credential","credentials","private_key"]),x=[/^[^\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_-]+$/]}}),N=I({"src/middleware/rate-limiter.ts"(){C=60,D=6e4}});function W(e){return M.get(e)}var V=I({"src/core/tool-catalog.ts"(){H=new Set(["atoms_status","atoms_list_projects"]),A=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_create_variable","atoms_update_variable","atoms_delete_variable","atoms_create_domain","atoms_update_domain","atoms_delete_domain"]),U=new Set(["atoms_delete_item","atoms_delete_variable","atoms_delete_domain"]),q=new Set(["atoms_bulk_import"]),R={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_record_test_result","atoms_project_summary"],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"]},P=Object.keys(R),M=new Map;for(const[e,t]of Object.entries(R))for(const r of t)M.set(r,e)}});function L(){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)P.includes(e)?r.add(e):i.push(e);return{allowed:r,unknown:i}}function F(){const e=process.env.ATOMS_MCP_READ_ONLY;return"1"===e||"true"===e?.toLowerCase()}function J(e){if(F()&&A.has(e))return!1;if(H.has(e))return!0;const t=L();if(null===t)return!0;const r=W(e);return!!r&&t.allowed.has(r)}var z,B,Q,G=I({"src/middleware/tool-registry.ts"(){V()}});function Y(){const e=process.env.ATOMS_MCP_PROJECT_ID?.trim();return e?z.test(e)?e:(B||(process.stderr.write(`[atoms-mcp] WARNING: ATOMS_MCP_PROJECT_ID="${e.slice(0,50)}" is not a valid UUID — scope ignored.\n`),B=!0),null):null}var K,Z,X=I({"src/middleware/project-scope.ts"(){z=/^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i,B=!1,Q=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}}}}),ee=I({"src/core/types.ts"(){K={read_only:!1,lockdown:!1,block_destructive:!1,block_bulk_import:!1,cross_project_browse:!0,allowed_toolsets:["items","traceability","coverage","variables","domains"],forbidden_tools:[],project_scope:null,require_confirmation_for:[]}}});function te(){return Z}var re=I({"src/middleware/session-policy.ts"(){ee(),Z=K}});function ie(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 ne,ae,oe=I({"src/core/policy.ts"(){V()}}),se={};async function de(){try{const e=await t(ae,"utf-8"),r=JSON.parse(e);return r.access_token&&r.refresh_token?r:null}catch{return null}}async function ce(e){await r(ne,{recursive:!0,mode:448}),await i(ae,JSON.stringify(e,null,2),{mode:384})}async function le(){const e=await de();return!!e&&e.expires_at>Date.now()+6e4}function me(e){return e.expires_at>Date.now()+6e4}async function pe(){try{await n(ae)}catch{}}function ue(){return ae}E(se,{clearCredentials:()=>pe,getCredentialsPath:()=>ue,hasValidCredentials:()=>le,isTokenValid:()=>me,readCredentials:()=>de,writeCredentials:()=>ce});var _e,fe,he,ge=I({"src/auth/token-store.ts"(){ne=s(a(),".atoms"),ae=s(ne,"credentials.json")}}),ye={};E(ye,{ATOMS_APP_URL:()=>he,ATOMS_SUPABASE_ANON_KEY:()=>fe,ATOMS_SUPABASE_URL:()=>_e});var be=I({"src/config.ts"(){_e="https://gmebjyhomsbvhrxffzre.supabase.co",fe="sb_publishable_b49MUAB8XCrQiF7x5b9lUA_w1aplSBH",he=process.env.ATOMS_APP_URL??"https://x.atoms.tech"}}),we={};async function ve(){const e=process.env.ATOMS_ACCESS_TOKEN;if(e){const t=je(e);return{access_token:e,refresh_token:"",user_id:t.sub,email:t.email??""}}const t=await de();if(!t)throw new Error("Not authenticated. 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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:"mcp_claude",session_id:ti()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),et(We({id:e.item_id,title:i.title,type:i.type,restored:!0,message:`Item ${e.item_id} restored successfully.`}))}catch(e){return tt(Ke(e))}}E(Xt,{restoreItemHandler:()=>er});var tr,rr,ir=I({"src/tools/restore-item.ts"(){Me(),ni(),it()}}),nr={};async function ar(e){try{const t=await Te(),r=Ce();try{await He(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return tt(Je("Viewer"));throw e}const i=async(i,n,a)=>{const o=await ot(t,e.project_id,i.from_id);if(!o)throw new Error(`Item "${i.from_id}" not found`);const s=await ot(t,e.project_id,i.to_id);if(!s)throw new Error(`Item "${i.to_id}" not found`);const d=tr(i.type);if("add"===i.action){const{data:n}=await t.from("item_relationships").select("from_id").eq("from_id",i.from_id).eq("to_id",i.to_id).eq("type",i.type).eq("project_id",e.project_id).maybeSingle();if(!n){const{error:r}=await t.from("item_relationships").insert({from_id:i.from_id,to_id:i.to_id,type:i.type,project_id:e.project_id});if(r)throw new Error(r.message)}const a=JSON.parse(JSON.stringify(o.data));a.relationships=a.relationships??{};const c=a.relationships[rr(i.type)]??[];c.includes(i.to_id)||(a.relationships[rr(i.type)]=[...c,i.to_id]),await t.from("items").update({data:a,updated_by:r}).eq("id",i.from_id).eq("project_id",e.project_id);const l=JSON.parse(JSON.stringify(s.data));l.relationships=l.relationships??{};const m=l.relationships[rr(d)]??[];m.includes(i.from_id)||(l.relationships[rr(d)]=[...m,i.from_id]),await t.from("items").update({data:l,updated_by:r}).eq("id",i.to_id).eq("project_id",e.project_id)}else{await Promise.all([t.from("item_relationships").delete().eq("from_id",i.from_id).eq("to_id",i.to_id).eq("type",i.type).eq("project_id",e.project_id),t.from("item_relationships").delete().eq("from_id",i.to_id).eq("to_id",i.from_id).eq("type",d).eq("project_id",e.project_id)]);const n=JSON.parse(JSON.stringify(o.data));n.relationships?.[rr(i.type)]&&(n.relationships[rr(i.type)]=n.relationships[rr(i.type)].filter(e=>e!==i.to_id)),await t.from("items").update({data:n,updated_by:r}).eq("id",i.from_id).eq("project_id",e.project_id);const a=JSON.parse(JSON.stringify(s.data));a.relationships?.[rr(d)]&&(a.relationships[rr(d)]=a.relationships[rr(d)].filter(e=>e!==i.from_id)),await t.from("items").update({data:a,updated_by:r}).eq("id",i.to_id).eq("project_id",e.project_id)}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:"mcp_claude",session_id:ti()};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: ${e.message}\n`)})};if(e.operations&&Array.isArray(e.operations)){for(const t of e.operations)if(t.from_id===t.to_id)return tt(ze(`Self-reference in batch: "${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)),o=r.filter(e=>!a.has(e));if(o.length>0)return tt(Fe("Items",o.join(", ")));const{data:s}=await t.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id),d=new Map;for(const e of 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t.from("items").insert(d);if(l)for(const{itemId:e,input:r,index:i}of s){const n=d.find(t=>t.id===e);if(!n)continue;const{error:s}=await t.from("items").insert(n);s?o.push({index:i,title:r.title,error:s.message}):a.push({id:e,title:r.title,type:r.type})}else for(const{itemId:e,input:t}of s)a.push({id:e,title:t.title,type:t.type});const m=s.filter(({input:e})=>e.parent_id).filter(({itemId:e})=>a.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}));m.length>0&&await t.from("item_relationships").insert(m).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: bulk relationship sync failed: ${e.message}\n`)});const p=a.map(t=>({item_id:t.id,project_id:e.project_id,changed_by:r,event_type:"created",old_data:null,new_data:c.get(t.id)??null,actor:"mcp_claude",session_id:n}));return p.length>0&&await t.from("change_history").insert(p).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: bulk change_history log failed: ${e.message}\n`)}),et(We({created:a.length,items:a,errors:o.length>0?o:[],project_id:e.project_id}))}catch(e){return tt(Ke(e))}}E(sr,{bulkImportHandler:()=>dr});var cr=I({"src/tools/bulk-import.ts"(){Me(),ct(),ni(),Gt(),it()}}),lr={};async function mr(e){try{const t=await Te(),r=Ce(),i=De();try{await He(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return tt(Je("Viewer"));throw e}const n=await ot(t,e.project_id,e.item_id);if(!n)return tt(Fe("Item",e.item_id));if("test-case"!==n.type)return tt(ze(`Item '${e.item_id}' is a ${n.type}, not a test-case`));const a=(new Date).toISOString(),{error:o}=await t.from("test_results").insert({item_id:e.item_id,project_id:e.project_id,result:e.result,run_by:i||r,run_at:a,note:e.note??null});if(o)throw new Error(o.message);return 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:a,note:e.note},actor:"mcp_claude",session_id:ti()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),et(We({item_id:e.item_id,result:e.result,run_at:a,run_by:i||r,note:e.note??null,message:`Test result '${e.result}' recorded for ${e.item_id}`}))}catch(e){return tt(Ke(e))}}E(lr,{recordTestResultHandler:()=>mr});var pr,ur,_r,fr,hr=I({"src/tools/record-test-result.ts"(){Me(),ct(),ni(),it()}}),gr={};async function yr(e){try{const t=Math.min(Math.max(e.depth??5,1),10),r=await Te(),i=await ot(r,e.project_id,e.item_id);if(!i)return tt(Fe("Item",e.item_id));const{data:n,error:a}=await r.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(a)throw new Error(a.message);const{data:o,error:s}=await r.from("items").select("id, title, 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Qr,Gr,Yr,Kr,Zr=I({"src/tools/impact-analysis.ts"(){Me(),ct(),it(),Wr=200,Vr=["parent","verifies","traces_to","allocated_from","decomposed_from"],Lr=["child","verified_by","allocated_to","decomposes_to","traced_by"],Fr={parent:"child",child:"parent",verifies:"verified_by",verified_by:"verifies",related:"related",traces_to:"traced_by",traced_by:"traces_to",allocated_to:"allocated_from",allocated_from:"allocated_to",decomposes_to:"decomposed_from",decomposed_from:"decomposes_to"}}});function Xr(t){J(t.toolName)&&function(t,r){const i=`ui://${r.toolName}/${r.htmlFile}`,n=function(e,t){const r=u(import.meta.url),i=o.dirname(r);return o.resolve(i,"apps","src","apps",e,t)}(r.appName,r.htmlFile),a=[...rt.resourceDomains,...r.extraResourceDomains??[]];c(t,r.toolName,{title:r.title,description:r.description,inputSchema:r.inputSchema,annotations:r.annotations,_meta:{ui:{resourceUri:i}}},r.handler),l(t,`${r.title} UI`,i,{mimeType:m},async()=>{const t=await 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r=e.project_id;if("string"==typeof r&&r!==t)throw new Q(t,r)}(r)}catch(e){if(e instanceof Q)return tt(Qe(e.expectedProjectId));throw e}{const e=te(),t=r?.project_id;if(null!==e.project_scope&&"string"==typeof t&&!e.project_scope.includes(t))return tt(Le("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 Te(),n=Ce()}catch{return t(r)}const o=await async function(e,t){const r=parseInt(process.env.ATOMS_RATE_LIMIT_RPM??"",10)||C,i=new Date,n=new Date(i.getTime()-D);try{const{count:a,error:o}=await t.from("mcp_rate_limits").select("id",{count:"exact",head:!0}).eq("user_id",e).gte("requested_at",n.toISOString());if(o)throw new Error(o.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 o=(r?new Date(r.requested_at).getTime():i.getTime())+D-i.getTime();return{allowed:!1,retryAfterSeconds:Math.max(1,Math.ceil(o/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: ${e.message}\n`)});const s=new Date(i.getTime()-2*D);return t.from("mcp_rate_limits").delete().eq("user_id",e).lt("requested_at",s.toISOString()).then(()=>{}),{allowed:!0}}catch(e){return process.stderr.write(`[rate-limiter] DB check failed (${e instanceof Error?e.message:String(e)}), falling back to allow.\n`),{allowed:!0}}}(n,a);if(!o.allowed)return tt(Ge(o.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(()=>(Me(),Oe));await t(a,e)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message){const{accessDeniedError:e}=await Promise.resolve().then(()=>(it(),$e));return tt(e("Viewer (lockdown mode: read access requires editor or admin)"))}}}const s=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:s(),error_msg:d,project_id:r.project_id,session_id:Yr,client_name:Kr};try{!function(e,t,r){const i=T(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: ${e.message}\n`)})}(await Te(),n,t)}catch{}}}}function ti(){return Yr}var ri,ii,ni=I({"src/server.ts"(){$(),N(),G(),X(),re(),oe(),Me(),it(),nt(),Qr=new y({name:"atoms-mcp-server",version:"0.5.0"}),Gr=(e,t,r)=>{if(J(e))return Qr.registerTool(e,t,r)},Yr=f(),Kr=process.env.ATOMS_CLIENT_NAME??"unknown",Gr("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(()=>(ge(),se)),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(()=>(Ee(),we)),{email:t}=await e();return{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)}]}}}),Gr("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}},ei("atoms_list_projects",async()=>{const{listProjectsHandler:e}=await Promise.resolve().then(()=>(pt(),lt));return e()})),Gr("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:b.string().uuid("Must be a valid project UUID").describe("UUID of the project"),type:b.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),domain:b.string().max(64).optional().describe("Filter by domain tag (e.g., 'Safety', 'Performance')"),level:b.string().max(32).optional().describe("Filter by level (System, Subsystem, Component)"),limit:b.number().int().min(1).max(200).default(50).describe("Max results (default 50, max 200)"),offset:b.number().int().min(0).default(0).describe("Pagination offset (default 0)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_list_items",async e=>{const{listItemsHandler:t}=await Promise.resolve().then(()=>(ft(),ut));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Item ID (e.g., REQ-001)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_get_item",async e=>{const{getItemHandler:t}=await Promise.resolve().then(()=>(yt(),ht));return t(e)})),Gr("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 - 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")',inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),query:b.string().min(1).max(1e3).describe("Search text"),type:b.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),limit:b.number().int().min(1).max(100).default(25).describe("Max results (default 25, max 100)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_search",async e=>{const{searchHandler:t}=await Promise.resolve().then(()=>(vt(),bt));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project"),query:b.string().min(1).max(1e3).describe("Natural-language concept query"),type:b.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),limit:b.number().int().min(1).max(50).default(10).describe("Max results (default 10, max 50)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_semantic_search",async e=>{const{semanticSearchHandler:t}=await Promise.resolve().then(()=>(St(),jt));return t(e)})),Xr({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\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")',inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),domain:b.string().max(64).optional().describe("Filter by domain tag"),level:b.string().max(32).optional().describe("Filter by level")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:ei("atoms_get_coverage",async e=>{const{getCoverageHandler:t}=await Promise.resolve().then(()=>(Et(),kt));return t(e)})}),Gr("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_claude) 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:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Item ID"),limit:b.number().int().min(1).max(100).default(20).describe("Max entries (default 20)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_get_history",async e=>{const{getHistoryHandler:t}=await Promise.resolve().then(()=>(Ct(),Ot));return t(e)})),Xr({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\nReturns:\n Mermaid graph string.",inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),root_item_id:b.string().max(20).optional().describe("Root item ID to start from"),depth:b.number().int().min(1).max(10).default(3).describe("Max depth"),include_tests:b.boolean().default(!0).describe("Include test case links")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},extraResourceDomains:["cdn.jsdelivr.net","mermaid.ink"],handler:ei("atoms_export_mermaid",async e=>{const{exportMermaidHandler:t}=await Promise.resolve().then(()=>(Ut(),Dt));return t(e)})}),Gr("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\nReturns:\n Created item with generated ID (e.g., \"REQ-058\")\n\nSide effects:\n - Logs to change_history with actor='mcp_claude'\n - Creates relationships if parent_ids provided",inputSchema:{project_id:b.string().uuid().describe("UUID of the target project"),type:b.enum(["requirement","test-case","note"]).describe("Item type"),title:b.string().min(1).max(500).describe("Item title"),body:b.string().max(5e4).optional().describe("Rich text body"),summary:b.string().max(2e3).optional().describe("Brief summary"),domains:b.array(b.string().max(64)).max(20).optional().describe("Domain tags"),level:b.string().max(32).optional().describe("System|Subsystem|Component"),parent_ids:b.array(b.string().max(20)).max(50).optional().describe("Parent item IDs to link"),echo:b.boolean().optional().describe("false → lean {id,type} response, saves ~580 tokens")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},ei("atoms_create_item",async e=>{const{createItemHandler:t}=await Promise.resolve().then(()=>(Pt(),qt));return t(e)})),Gr("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\nReturns:\n Updated item.",inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).optional().describe("Item ID (single form)"),title:b.string().min(1).max(500).optional().describe("New title"),body:b.string().max(5e4).optional().describe("New body"),summary:b.string().max(2e3).optional().describe("New summary"),domains:b.array(b.string().max(64)).max(20).optional().describe("New domain tags"),level:b.string().max(32).optional().describe("New level"),status:b.enum(["passed","failed","blocked","not-run"]).optional().describe("Test case status"),echo:b.boolean().optional().describe("false → lean {id,updated_fields} response, saves ~580 tokens"),reason:b.string().max(500).optional().describe("Change rationale, persisted in audit history"),updates:b.array(b.object({item_id:b.string().min(1).max(20),title:b.string().min(1).max(500).optional(),body:b.string().max(5e4).optional(),summary:b.string().max(2e3).optional(),domains:b.array(b.string().max(64)).max(20).optional(),level:b.string().max(32).optional(),status:b.enum(["passed","failed","blocked","not-run"]).optional()})).optional().describe("Array form: update many items in one call"),idempotency_key:b.string().max(128).optional().describe("Safe retry key (24h TTL)"),continue_on_error:b.boolean().optional().describe("Allow partial success (default false = atomic)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_update_item",async e=>{const{updateItemHandler:t}=await Promise.resolve().then(()=>(Vt(),Mt));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Item ID to soft-delete"),confirmation_token:b.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}},ei("atoms_delete_item",async e=>{const{deleteItemHandler:t}=await Promise.resolve().then(()=>(Zt(),Yt));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project"),item_id:b.string().max(256).describe("ID of the soft-deleted item to restore")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_restore_item",async e=>{const{restoreItemHandler:t}=await Promise.resolve().then(()=>(ir(),Xt));return t(e)})),Gr("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\nReturns:\n Updated relationship state for both items.",inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),from_id:b.string().min(1).max(20).optional().describe("Source item ID (single form)"),to_id:b.string().min(1).max(20).optional().describe("Target item ID (single form)"),type:b.enum(["parent","child","related","verifies","verified_by"]).optional().describe("Relationship type"),action:b.enum(["add","remove"]).optional().describe("Add or remove"),echo:b.boolean().optional().describe("false → lean response"),reason:b.string().max(500).optional().describe("Change rationale, persisted in audit history"),operations:b.array(b.object({action:b.enum(["add","remove"]),from_id:b.string().min(1).max(20),to_id:b.string().min(1).max(20),type:b.enum(["parent","child","related","verifies","verified_by"])})).optional().describe("Array form: batch relationship ops. Always atomic with DAG cycle detection."),idempotency_key:b.string().max(128).optional().describe("Safe retry key (24h TTL)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_link_items",async e=>{const{linkItemsHandler:t}=await Promise.resolve().then(()=>(or(),nr));return t(e)})),Xr({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_claude' for each created item\n - Creates parent relationships for items with parent_id",inputSchema:{project_id:b.string().uuid().describe("UUID of the target project"),items:b.array(b.object({type:b.enum(["requirement","test-case","note"]).describe("Item type"),title:b.string().min(1).max(500).describe("Item title"),body:b.string().max(5e4).optional().describe("Rich text body"),summary:b.string().max(2e3).optional().describe("Brief summary"),domains:b.array(b.string().max(64)).max(20).optional().describe("Domain tags"),level:b.string().max(32).optional().describe("System|Subsystem|Component"),parent_id:b.string().max(20).optional().describe("Parent item ID to link")})).min(1).max(100).describe("Items to create (1-100)"),confirmation_token:b.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:ei("atoms_bulk_import",async e=>{const{bulkImportHandler:t}=await Promise.resolve().then(()=>(cr(),sr));return t(e)})}),Gr("atoms_record_test_result",{title:"Record Test Result",description:"Record a pass/fail/blocked result for a test case.\n\nAppends to the test results history. 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\nReturns:\n Recorded result with timestamp.\n\nSide effects:\n - Appends to test_results table\n - Logs to change_history with actor='mcp_claude'",inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Test case ID (e.g., TC-001)"),result:b.enum(["passed","failed","blocked","not-run"]).describe("Test result"),note:b.string().max(1e3).optional().describe("Reason or comment for this result")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},ei("atoms_record_test_result",async e=>{const{recordTestResultHandler:t}=await Promise.resolve().then(()=>(hr(),lr));return t(e)})),Xr({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)\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:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Starting item ID"),direction:b.enum(["upstream","downstream","both"]).describe("Traversal direction"),depth:b.number().int().min(1).max(10).default(5).describe("Max traversal depth (default 5)"),relationship_types:b.array(b.enum(["parent","child","related","verifies","verified_by"])).optional().describe("Filter to specific relationship types")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:ei("atoms_trace",async e=>{const{traceHandler:t}=await Promise.resolve().then(()=>(br(),gr));return t(e)})}),Gr("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\nReturns:\n { variables: [{ id, name, value, unit, description }], total }",inputSchema:{project_id:b.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_list_variables",async e=>{const{listVariablesHandler:t}=await Promise.resolve().then(()=>(Ir(),wr));return t(e)})),Gr("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\nReturns:\n { variable, referenced_by: [{ id, title, type }], reference_count }',inputSchema:{project_id:b.string().uuid().describe("UUID of the project"),variable_name:b.string().min(1).max(64).describe("Variable name")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_get_variable",async e=>{const{getVariableHandler:t}=await Promise.resolve().then(()=>(Ir(),wr));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project"),variable_name:b.string().min(1).max(64).describe("Variable name"),value:b.string().max(500).optional().describe("New value"),unit:b.string().max(32).optional().describe("Unit abbreviation"),description:b.string().max(2e3).optional().describe("Description")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_update_variable",async e=>{const{updateVariableHandler:t}=await Promise.resolve().then(()=>(Ir(),wr));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project"),name:b.string().min(1).max(64).optional().describe("Variable name (single form)"),value:b.string().min(1).max(500).optional().describe("Initial value (single form)"),unit:b.string().max(32).optional().describe("Unit abbreviation"),description:b.string().max(2e3).optional().describe("Description"),echo:b.boolean().optional().describe("false → lean response (default true)"),variables:b.array(b.object({name:b.string().min(1).max(64).describe("Variable name"),value:b.string().min(1).max(500).describe("Initial value"),unit:b.string().max(32).optional().describe("Unit abbreviation"),description:b.string().max(2e3).optional().describe("Description")})).optional().describe("Array form: batch variable creation. Atomic — all or none."),idempotency_key:b.string().max(128).optional().describe("Dedup key for retries")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},ei("atoms_create_variable",async e=>{const{createVariableHandler:t}=await Promise.resolve().then(()=>(Ir(),wr));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project"),name:b.string().min(1).max(64).describe("Variable name to delete"),force:b.boolean().optional().describe("Delete even if items reference it (default false)"),confirmation_token:b.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}},ei("atoms_delete_variable",async e=>{const{deleteVariableHandler:t}=await Promise.resolve().then(()=>(Ir(),wr));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_list_domains",async e=>{const{listDomainsHandler:t}=await Promise.resolve().then(()=>(Ur(),Er));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project"),name:b.string().min(1).max(64).describe("Domain name")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},ei("atoms_create_domain",async e=>{const{createDomainHandler:t}=await Promise.resolve().then(()=>(Ur(),Er));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project"),name:b.string().min(1).max(64).describe("Current domain name"),new_name:b.string().min(1).max(64).describe("New domain name"),dry_run:b.boolean().optional().describe("Preview impact without applying (default false)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},ei("atoms_update_domain",async e=>{const{updateDomainHandler:t}=await Promise.resolve().then(()=>(Ur(),Er));return t(e)})),Gr("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:b.string().uuid().describe("UUID of the project"),name:b.string().min(1).max(64).describe("Domain name to delete"),force:b.boolean().optional().describe("Strip from all items and delete (default false)"),confirmation_token:b.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}},ei("atoms_delete_domain",async e=>{const{deleteDomainHandler:t}=await Promise.resolve().then(()=>(Ur(),Er));return t(e)})),Xr({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:b.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:ei("atoms_project_summary",async e=>{const{projectSummaryHandler:t}=await Promise.resolve().then(()=>(Mr(),qr));return t(e)})}),Xr({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:b.string().uuid().describe("UUID of the project"),type:b.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),domain:b.string().max(64).optional().describe("Filter by domain tag"),level:b.string().max(32).optional().describe("Filter by level (System, Subsystem, Component)"),query:b.string().max(1e3).optional().describe("Full-text search query"),limit:b.number().int().min(1).max(100).default(25).describe("Max results (default 25, max 100)"),offset:b.number().int().min(0).default(0).describe("Pagination offset (default 0)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:ei("atoms_browse",async e=>{const{browseHandler:t}=await Promise.resolve().then(()=>(Jr(),$r));return t(e)})}),Gr("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:b.string().uuid().describe("UUID of the project"),item_id:b.string().min(1).max(20).describe("Item ID to analyze (e.g., REQ-001)"),direction:b.enum(["downstream","upstream","both"]).default("downstream").describe("Traversal direction (default: downstream)"),depth:b.number().int().min(1).optional().describe("Max traversal depth. Omit for full depth."),include_variable_refs:b.boolean().default(!0).describe("Reserved for variable-aware impact (future). Default true.")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},ei("atoms_impact_analysis",async e=>{const{impactAnalysisHandler:t}=await Promise.resolve().then(()=>(Zr(),zr));return t(e)}))}}),ai={};async function oi(){const e=h(32).toString("base64url"),t=g("sha256").update(e).digest("base64url"),r=`http://localhost:${ri}${ii}`,i=new p(`${he}/auth/mcp-consent`);return i.searchParams.set("redirect_uri",r),i.searchParams.set("code_challenge",t),i.searchParams.set("code_challenge_method","S256"),new Promise((t,r)=>{let n;function a(){clearTimeout(n)}const o=w(async(i,n)=>{const s=new p(i.url??"/",`http://localhost:${ri}`);if(s.pathname!==ii)return n.writeHead(404),void n.end("Not found");try{if("access_denied"===s.searchParams.get("error"))return n.writeHead(200,{"Content-Type":"text/html"}),n.end(di("Authorization was cancelled.")),a(),o.close(),void r(new Error("Authorization cancelled by user."));const i=s.searchParams.get("code");if(i){const s=await fetch(`${_e}/auth/v1/token?grant_type=pkce`,{method:"POST",headers:{"Content-Type":"application/json",apikey:fe},body:JSON.stringify({auth_code:i,code_verifier:e})}),d=await s.json();if(!s.ok||!d.access_token){const e=d.error_description??d.msg??"Unknown error";return n.writeHead(200,{"Content-Type":"text/html"}),n.end(di(`Code exchange failed: ${e}`)),a(),o.close(),void r(new Error(`Code exchange failed: ${e}`))}let c="authenticated";try{c=JSON.parse(Buffer.from(d.access_token.split(".")[1],"base64").toString()).email??c}catch{}const{createClient:l}=await import("@supabase/supabase-js"),m=l(_e,fe,{global:{headers:{Authorization:`Bearer ${d.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(di('No ATOMS account found for this Google account.<br><br>Please sign up at <a href="https://x.atoms.tech">x.atoms.tech</a> first, then run this login command again.')),a(),o.close(),void r(new Error("No ATOMS account found. Sign up at x.atoms.tech first."))):(await ce({access_token:d.access_token,refresh_token:d.refresh_token,expires_at:Date.now()+1e3*(d.expires_in??3600),user_email:c}),n.writeHead(200,{"Content-Type":"text/html"}),n.end(si(c)),a(),o.close(),void t({email:c}))}const d=s.searchParams.get("access_token"),c=s.searchParams.get("refresh_token"),l=parseInt(s.searchParams.get("expires_in")??"3600",10);d&&c?(await ce({access_token:d,refresh_token:c,expires_at:Date.now()+1e3*l}),n.writeHead(200,{"Content-Type":"text/html"}),n.end(si("authenticated")),a(),o.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"),a(),o.close(),r(e)}});o.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 ce({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})),a(),o.close(),t({email:e.user_email??"authenticated"})}catch(e){i.writeHead(500),i.end("Failed to store credentials"),a(),o.close(),r(e)}})}}),o.listen(ri,"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")}}),n=setTimeout(()=>{o.close(),r(new Error("Login timed out after 60 seconds. Run 'npx @atoms-tech/atoms-mcp login' to try again."))},6e4)})}function si(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 di(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>`}E(ai,{login:()=>oi});var ci=I({"src/auth/login.ts"(){ge(),be(),ri=19275,ii="/callback"}});ni(),G(),re(),Me(),ee();var li=process.argv.slice(2)[0];(async function(){switch(li){case"login":{const{login:e}=await Promise.resolve().then(()=>(ci(),ai));try{const{email:t}=await e();process.stderr.write(`\n [32m✓[0m Authenticated as ${t}\n`),process.stderr.write(" [32m✓[0m Credentials saved to ~/.atoms/credentials.json\n\n"),process.stderr.write(" [1mNext steps:[0m\n"),process.stderr.write(" [36m$[0m 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(' [90m{\n "mcpServers": {\n "atoms": {\n "command": "npx",\n "args": ["-y", "@atoms-tech/atoms-mcp"]\n }\n }\n }[0m\n\n')}catch(e){process.stderr.write(`\n [31m✗[0m ${e instanceof Error?e.message:String(e)}\n\n`),process.exit(1)}break}case"whoami":{const{getValidToken:e}=await Promise.resolve().then(()=>(Ee(),we));try{const{email:t,user_id:r}=await e();process.stderr.write(`\n [32m✓[0m Logged in as ${t}\n [90mUser ID: ${r}[0m\n\n`)}catch(e){process.stderr.write("\n [31m✗[0m Not authenticated.\n Run: npx @atoms-tech/atoms-mcp login\n\n"),process.exit(1)}break}case"logout":{const{clearCredentials:e}=await Promise.resolve().then(()=>(ge(),se));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 v0.4.0\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");try{const{getValidToken:e}=await Promise.resolve().then(()=>(Ee(),we)),{email:t}=await e();process.stderr.write(`[atoms-mcp] Authenticated as ${t}\n`)}catch{process.stderr.write("[atoms-mcp] No credentials found. Starting login flow...\n");try{const{login:e}=await Promise.resolve().then(()=>(ci(),ai)),{email:t}=await e();process.stderr.write(`[atoms-mcp] Authenticated as ${t}\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`)}}process.stderr.write(`[atoms-mcp] Tool registry: ${function(){const e=F(),t=L(),r=[];r.push(e?"read-only":"read+write"),null===t?r.push("all toolsets"):(r.push(`toolsets=${[...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`);try{const t=await Te(),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: ${n.message}\n`),null):i?.org_id??null}(t,r),n=await async function(e,t,r){if(!r)return{role:null,is_member:!1,effective:K};const{data:i,error:n}=await e.rpc("mcp_resolve_policy",{p_user_id:t,p_org_id:r});return n?(process.stderr.write(`[atoms-mcp] mcp_resolve_policy failed (${n.code}): ${n.message}. Falling back to permissive policy.\n`),{role:null,is_member:!1,effective:K}):function(e){if(!e||"object"!=typeof e)return{role:null,is_member:!1,effective:K};const t=e,r="string"==typeof t.role?t.role:null,i=!0===t.is_member,n=t.effective??{},a=(e,t)=>Array.isArray(e)?e.filter(e=>"string"==typeof e):t,o=(e,t)=>"boolean"==typeof e?e:t,s=n.project_scope,d=Array.isArray(s)&&s.length>0?s.filter(e=>"string"==typeof e):null;return{role:r,is_member:i,effective:{read_only:o(n.read_only,K.read_only),lockdown:o(n.lockdown,K.lockdown),block_destructive:o(n.block_destructive,K.block_destructive),block_bulk_import:o(n.block_bulk_import,K.block_bulk_import),cross_project_browse:o(n.cross_project_browse,K.cross_project_browse),allowed_toolsets:a(n.allowed_toolsets,K.allowed_toolsets),forbidden_tools:a(n.forbidden_tools,K.forbidden_tools),project_scope:d,require_confirmation_for:a(n.require_confirmation_for,K.require_confirmation_for)}}}(i)}(t,r,i);e={effective:n.effective,role:n.role,org_id:i},Z=e.effective,n.is_member&&i?process.stderr.write(`[atoms-mcp] Org policy loaded: org=${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`)}const t=new v;await Qr.connect(t),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)});
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