@atoms-tech/atoms-mcp 0.3.0 → 0.3.1

package/README.md

@@ -3,7 +3,7 @@
 MCP server for [ATOMS.tech](https://atoms.tech) — connect AI agents to your requirements management workspace.
 
 [![npm version](https://img.shields.io/npm/v/@atoms-tech/atoms-mcp)](https://www.npmjs.com/package/@atoms-tech/atoms-mcp)
-[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+[![License: Proprietary](https://img.shields.io/badge/License-Proprietary-red.svg)](https://atoms.tech)
 
 ## Quick Start
 

package/dist/index.cjs

@@ -0,0 +1,2 @@
+#!/usr/bin/env node
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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: ${e.message}\n`)}),ie(Y({created:a.length,items:a,errors:s.length>0?s:[],project_id:e.project_id}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?ae(re()):ae(ne(e instanceof Error?e.message:String(e)))}}x(Ve,{bulkImportHandler:()=>Ge});var Qe=j({"src/tools/bulk-import.ts"(){Q(),pe(),gt(),oe()}}),Ye={};async function Ke(e){try{const t=await J(),r=B(),n=W??"";try{await V(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return ae(ee("Viewer"));throw e}const i=await le(t,e.project_id,e.item_id);if(!i)return ae(Z("Item",e.item_id));if("test-case"!==i.type)return ae(te(`Item '${e.item_id}' is a ${i.type}, not a test-case`));const a=(new Date).toISOString(),{error:s}=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(s)throw new Error(s.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:ut()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),ie(Y({item_id:e.item_id,result:e.result,run_at:a,run_by:n||r,note:e.note??null,message:`Test result '${e.result}' recorded for ${e.item_id}`}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?ae(re()):ae(ne(e instanceof Error?e.message:String(e)))}}x(Ye,{recordTestResultHandler:()=>Ke});var Xe,Ze,et,tt,rt=j({"src/tools/record-test-result.ts"(){Q(),pe(),gt(),oe()}}),nt={};async function it(e){try{const t=Math.min(Math.max(e.depth??5,1),10),r=await J();if(!await le(r,e.project_id,e.item_id))return ae(Z("Item",e.item_id));const{data:n,error:i}=await r.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(i)throw new Error(i.message);const{data:a,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 o=new Map;for(const e of a??[])o.set(e.id,{title:e.title,type:e.type});const d=new Map,c=(e,t,r)=>{d.has(e)||d.set(e,[]),d.get(e).push({neighbor:t,relType:r})},l=e.relationship_types?new Set(e.relationship_types):null;for(const t of n??[]){const r=t.type;if(("upstream"===e.direction||"both"===e.direction)&&(Ze.includes(r)&&(l&&!l.has(r)||c(t.from_id,t.to_id,r)),et.includes(r))){const e=tt[r]??r;l&&!l.has(e)||c(t.to_id,t.from_id,e)}if(("downstream"===e.direction||"both"===e.direction)&&(et.includes(r)&&(l&&!l.has(r)||c(t.from_id,t.to_id,r)),Ze.includes(r))){const e=tt[r]??r;l&&!l.has(e)||c(t.to_id,t.from_id,e)}"related"===r&&(l&&!l.has("related")||(c(t.from_id,t.to_id,"related"),c(t.to_id,t.from_id,"related")))}const m=new Set;m.add(e.item_id);const p=[],u=[],h=d.get(e.item_id)??[];for(const e of h)u.push({id:e.neighbor,depth:1,relType:e.relType});for(;u.length>0&&p.length<Xe;){const{id:e,depth:r,relType:n}=u.shift();if(m.has(e)||r>t)continue;m.add(e);const i=o.get(e);if(i&&(p.push({id:e,title:i.title,type:i.type,relationship:n,depth:r}),r<t)){const t=d.get(e)??[];for(const e of t)m.has(e.neighbor)||u.push({id:e.neighbor,depth:r+1,relType:e.relType})}}return ie(Y({root:e.item_id,direction:e.direction,depth_limit:t,items:p,total_count:p.length,...p.length>=Xe?{truncated:!0,truncation_message:`Results capped at ${Xe} items. 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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}},pt("atoms_list_projects",async()=>{const{listProjectsHandler:e}=await Promise.resolve().then(()=>(_e(),ue));return e()})),dt.registerTool("atoms_list_items",{title:"List ATOMS Items",description:'List items in an ATOMS project with optional type/domain/level filters.\n\nThis is the primary ENTRY POINT for discovering items. Use it to browse\nproject contents before drilling into specific items with atoms_get_item.\n\nArgs:\n  - project_id (string, UUID): The project to list items from\n  - type (string, optional): Filter: requirement|test-case|note|table\n  - domain (string, optional): Filter by domain tag\n  - level (string, optional): Filter by level (System, Subsystem, Component)\n  - limit (number, optional): Max results, 1-200 (default 50)\n  - offset (number, optional): Pagination offset (default 0)\n\nReturns:\n  { status: "success", data: [{ id, title, type, status, domains, level }], meta: { total_count, limit, offset, has_more } }\n\nExamples:\n  - "Show me all requirements" → atoms_list_items(project_id, type="requirement")\n  - "What test cases exist?" → atoms_list_items(project_id, type="test-case")\n\nErrors:\n  - "Project not found" → verify project_id\n  - "Access denied" → check org membership',inputSchema:{project_id:o.z.string().uuid("Must be a valid project UUID").describe("UUID of the project"),type:o.z.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),domain:o.z.string().optional().describe("Filter by domain tag (e.g., 'Safety', 'Performance')"),level:o.z.string().optional().describe("Filter by level (System, Subsystem, Component)"),limit:o.z.number().int().min(1).max(200).default(50).describe("Max results (default 50, max 200)"),offset:o.z.number().int().min(0).default(0).describe("Pagination offset (default 0)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},pt("atoms_list_items",async e=>{const{listItemsHandler:t}=await Promise.resolve().then(()=>(ye(),ge));return t(e)})),dt.registerTool("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-00001", "TC-00050")\n\nReturns:\n  Full WorkItem with relationships, test runs, ownership, metadata.\n\nExamples:\n  - "Show me requirement REQ-00001" → atoms_get_item(project_id, "REQ-00001")\n  - "Get test case details" → atoms_get_item(project_id, "TC-00050")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID (e.g., REQ-00001)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},pt("atoms_get_item",async e=>{const{getItemHandler:t}=await Promise.resolve().then(()=>(ve(),we));return t(e)})),dt.registerTool("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:o.z.string().uuid().describe("UUID of the project"),query:o.z.string().min(1).max(1e3).describe("Search text"),type:o.z.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),limit:o.z.number().int().min(1).max(100).default(25).describe("Max results (default 25, max 100)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},pt("atoms_search",async e=>{const{searchHandler:t}=await Promise.resolve().then(()=>(Se(),je));return t(e)})),de(dt,{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:o.z.string().uuid().describe("UUID of the project"),domain:o.z.string().optional().describe("Filter by domain tag"),level:o.z.string().optional().describe("Filter by level")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:pt("atoms_get_coverage",async e=>{const{getCoverageHandler:t}=await Promise.resolve().then(()=>(Ee(),Ie));return t(e)})}),dt.registerTool("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:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID"),limit:o.z.number().int().min(1).max(100).default(20).describe("Max entries (default 20)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},pt("atoms_get_history",async e=>{const{getHistoryHandler:t}=await Promise.resolve().then(()=>(He(),Te));return t(e)})),de(dt,{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:o.z.string().uuid().describe("UUID of the project"),root_item_id:o.z.string().optional().describe("Root item ID to start from"),depth:o.z.number().int().min(1).max(10).default(3).describe("Max depth"),include_tests:o.z.boolean().default(!0).describe("Include test case links")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},extraResourceDomains:["cdn.jsdelivr.net"],handler:pt("atoms_export_mermaid",async e=>{const{exportMermaidHandler:t}=await Promise.resolve().then(()=>(ze(),Ue));return t(e)})}),dt.registerTool("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-00058\")\n\nSide effects:\n  - Logs to change_history with actor='mcp_claude'\n  - Creates relationships if parent_ids provided",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the target project"),type:o.z.enum(["requirement","test-case","note"]).describe("Item type"),title:o.z.string().min(1).max(500).describe("Item title"),body:o.z.string().optional().describe("Rich text body"),summary:o.z.string().optional().describe("Brief summary"),domains:o.z.array(o.z.string()).optional().describe("Domain tags"),level:o.z.string().optional().describe("System|Subsystem|Component"),parent_ids:o.z.array(o.z.string()).optional().describe("Parent item IDs to link")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},pt("atoms_create_item",async e=>{const{createItemHandler:t}=await Promise.resolve().then(()=>(Re(),De));return t(e)})),dt.registerTool("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:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID to update"),title:o.z.string().min(1).max(500).optional().describe("New title"),body:o.z.string().optional().describe("New body"),summary:o.z.string().optional().describe("New summary"),domains:o.z.array(o.z.string()).optional().describe("New domain tags"),level:o.z.string().optional().describe("New level"),status:o.z.enum(["passed","failed","blocked","not-run"]).optional().describe("Test case status")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},pt("atoms_update_item",async e=>{const{updateItemHandler:t}=await Promise.resolve().then(()=>(Ne(),Pe));return t(e)})),dt.registerTool("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\nArgs:\n  - project_id (string, UUID): Project containing the item\n  - item_id (string): Item to delete\n\nReturns:\n  Confirmation with deleted item summary.",inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Item ID to soft-delete")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!0,openWorldHint:!1}},pt("atoms_delete_item",async e=>{const{deleteItemHandler:t}=await Promise.resolve().then(()=>(Fe(),$e));return t(e)})),dt.registerTool("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:o.z.string().uuid().describe("UUID of the project"),from_id:o.z.string().min(1).max(20).describe("Source item ID"),to_id:o.z.string().min(1).max(20).describe("Target item ID"),type:o.z.enum(["parent","child","related","verifies","verified_by"]).describe("Relationship type"),action:o.z.enum(["add","remove"]).describe("Add or remove the relationship")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},pt("atoms_link_items",async e=>{const{linkItemsHandler:t}=await Promise.resolve().then(()=>(Be(),Le));return t(e)})),de(dt,{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:o.z.string().uuid().describe("UUID of the target project"),items:o.z.array(o.z.object({type:o.z.enum(["requirement","test-case","note"]).describe("Item type"),title:o.z.string().min(1).max(500).describe("Item title"),body:o.z.string().optional().describe("Rich text body"),summary:o.z.string().optional().describe("Brief summary"),domains:o.z.array(o.z.string()).optional().describe("Domain tags"),level:o.z.string().optional().describe("System|Subsystem|Component"),parent_id:o.z.string().optional().describe("Parent item ID to link")})).min(1).max(100).describe("Items to create (1-100)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1},handler:pt("atoms_bulk_import",async e=>{const{bulkImportHandler:t}=await Promise.resolve().then(()=>(Qe(),Ve));return t(e)})}),dt.registerTool("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-00001\")\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:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Test case ID (e.g., TC-00001)"),result:o.z.enum(["passed","failed","blocked","not-run"]).describe("Test result"),note:o.z.string().max(1e3).optional().describe("Reason or comment for this result")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},pt("atoms_record_test_result",async e=>{const{recordTestResultHandler:t}=await Promise.resolve().then(()=>(rt(),Ye));return t(e)})),de(dt,{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-00003 verify?" or\n"if I change REQ-00001, 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-00003 verify?" → atoms_trace(project_id, "TC-00003", "upstream")\n  - "What\'s affected by REQ-00001?" → atoms_trace(project_id, "REQ-00001", "downstream")',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project"),item_id:o.z.string().min(1).max(20).describe("Starting item ID"),direction:o.z.enum(["upstream","downstream","both"]).describe("Traversal direction"),depth:o.z.number().int().min(1).max(10).default(5).describe("Max traversal depth (default 5)"),relationship_types:o.z.array(o.z.enum(["parent","child","related","verifies","verified_by"])).optional().describe("Filter to specific relationship types")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:pt("atoms_trace",async e=>{const{traceHandler:t}=await Promise.resolve().then(()=>(at(),nt));return t(e)})}),de(dt,{appName:"summary",htmlFile:"summary-app.html",toolName:"atoms_project_summary",title:"Project Compliance Summary",description:'One-call project health and compliance dashboard.\n\nReturns item counts by type, test execution status, requirement coverage\n(overall and by domain), and recent change activity.\n\nIn MCP App hosts (Claude, ChatGPT), renders an interactive dashboard with charts.\nFalls back to JSON for non-UI clients.\n\nArgs:\n  - project_id (string, UUID): Project to summarize\n\nReturns:\n  { project_name, counts, test_status, coverage, coverage_by_domain, recent_changes, last_updated }\n\nExamples:\n  - "Give me a compliance snapshot" → atoms_project_summary(project_id)\n  - "How\'s our test coverage?" → atoms_project_summary(project_id)',inputSchema:{project_id:o.z.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:pt("atoms_project_summary",async e=>{const{projectSummaryHandler:t}=await Promise.resolve().then(()=>(mt(),st));return t(e)})})}}),ft={};async function yt(){const e=d.randomBytes(32).toString("base64url"),t=d.createHash("sha256").update(e).digest("base64url"),r=`http://localhost:${ht}${_t}`,n=new a.URL(`${z}/auth/mcp-consent`);return n.searchParams.set("redirect_uri",r),n.searchParams.set("code_challenge",t),n.searchParams.set("code_challenge_method","S256"),new Promise((t,r)=>{const i=c.createServer(async(n,s)=>{const o=new a.URL(n.url??"/",`http://localhost:${ht}`);if(o.pathname!==_t)return s.writeHead(404),void s.end("Not found");try{if("access_denied"===o.searchParams.get("error"))return s.writeHead(200,{"Content-Type":"text/html"}),s.end(bt("Authorization was cancelled.")),i.close(),void r(new Error("Authorization cancelled by user."));const n=o.searchParams.get("code");if(n){const a=await fetch(`${O}/auth/v1/token?grant_type=pkce`,{method:"POST",headers:{"Content-Type":"application/json",apikey:q},body:JSON.stringify({auth_code:n,code_verifier:e})}),o=await a.json();if(!a.ok||!o.access_token){const e=o.error_description??o.msg??"Unknown error";return s.writeHead(200,{"Content-Type":"text/html"}),s.end(bt(`Code exchange failed: ${e}`)),i.close(),void r(new Error(`Code exchange failed: ${e}`))}let d="authenticated";try{d=JSON.parse(Buffer.from(o.access_token.split(".")[1],"base64").toString()).email??d}catch{}const{createClient:c}=await import("@supabase/supabase-js"),l=c(O,q,{global:{headers:{Authorization:`Bearer ${o.access_token}`}}}),{data:m,error:p}=await l.from("org_members").select("org_id").limit(1);return p||!m||0===m.length?(s.writeHead(200,{"Content-Type":"text/html"}),s.end(bt('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.')),i.close(),void r(new Error("No ATOMS account found. Sign up at x.atoms.tech first."))):(await T({access_token:o.access_token,refresh_token:o.refresh_token,expires_at:Date.now()+1e3*(o.expires_in??3600),user_email:d}),s.writeHead(200,{"Content-Type":"text/html"}),s.end(wt(d)),i.close(),void t({email:d}))}const a=o.searchParams.get("access_token"),d=o.searchParams.get("refresh_token"),c=parseInt(o.searchParams.get("expires_in")??"3600",10);a&&d?(await T({access_token:a,refresh_token:d,expires_at:Date.now()+1e3*c}),s.writeHead(200,{"Content-Type":"text/html"}),s.end(wt("authenticated")),i.close(),t({email:"authenticated"})):(s.writeHead(200,{"Content-Type":"text/html"}),s.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){s.writeHead(500),s.end("Authentication failed"),i.close(),r(e)}});i.on("request",async(e,n)=>{if("POST"===e.method&&"/token"===e.url){let a="";e.on("data",e=>{a+=e.toString()}),e.on("end",async()=>{try{const e=JSON.parse(a);await T({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})),i.close(),t({email:e.user_email??"authenticated"})}catch(e){n.writeHead(500),n.end("Failed to store credentials"),i.close(),r(e)}})}}),i.listen(ht,"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")}}),setTimeout(()=>{i.close(),r(new Error("Login timed out after 5 minutes"))},3e5)})}function wt(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 bt(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>`}x(ft,{login:()=>yt});var vt=j({"src/auth/login.ts"(){D(),M(),ht=19275,_t="/callback"}});gt();var jt=process.argv.slice(2)[0];(async function(){switch(jt){case"login":{const{login:e}=await Promise.resolve().then(()=>(vt(),ft));try{const{email:t}=await e();process.stderr.write(`\n  ✓ Authenticated as ${t}\n`),process.stderr.write("  ✓ Credentials saved to ~/.atoms/credentials.json\n\n"),process.stderr.write("  Next steps:\n"),process.stderr.write("  $ claude mcp add atoms -- npx -y @atoms-tech/atoms-mcp\n"),process.stderr.write("\n  Or add to Claude Desktop (Settings → MCP → Edit Config):\n"),process.stderr.write('  {\n    "mcpServers": {\n      "atoms": {\n        "command": "npx",\n        "args": ["-y", "@atoms-tech/atoms-mcp"]\n      }\n    }\n  }\n\n')}catch(e){process.stderr.write(`\n  ✗ ${e instanceof Error?e.message:String(e)}\n\n`),process.exit(1)}break}case"whoami":{const{getValidToken:e}=await Promise.resolve().then(()=>(L(),R));try{const{email:t,user_id:r}=await e();process.stderr.write(`\n  ✓ Logged in as ${t}\n  User ID: ${r}\n\n`)}catch(e){process.stderr.write("\n  ✗ Not authenticated.\n  Run: npx @atoms-tech/atoms-mcp login\n\n"),process.exit(1)}break}case"logout":{const{clearCredentials:e}=await Promise.resolve().then(()=>(D(),k));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 v0.1.0\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(()=>(L(),R)),{email:t}=await e();process.stderr.write(`[atoms-mcp] Authenticated as ${t}\n`)}catch(e){process.stderr.write(`[atoms-mcp] Warning: ${e instanceof Error?e.message:String(e)}\n[atoms-mcp] Some tools may fail without authentication.\n`)}const e=new l.StdioServerTransport;await dt.connect(e),process.stderr.write("[atoms-mcp] MCP server running. Waiting for tool calls...\n")}}})().catch(e=>{process.stderr.write(`[atoms-mcp] Fatal: ${e instanceof Error?e.message:String(e)}\n`),process.exit(1)});

package/dist/index.js

@@ -1,91 +1,2 @@
 #!/usr/bin/env node
-/**
- * ATOMS MCP Server — CLI Entry Point
- *
- * Commands:
- *   npx @atoms-tech/atoms-mcp           → Start MCP server (stdio transport)
- *   npx @atoms-tech/atoms-mcp login     → Authenticate with ATOMS.tech
- *   npx @atoms-tech/atoms-mcp whoami    → Show current user
- *   npx @atoms-tech/atoms-mcp --version → Show version
- */
-import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
-import { server } from "./server.js";
-const args = process.argv.slice(2);
-const command = args[0];
-async function main() {
-    switch (command) {
-        case "login": {
-            const { login } = await import("./auth/login.js");
-            try {
-                const { email } = await login();
-                process.stderr.write(`\n  \x1b[32m✓\x1b[0m Authenticated as ${email}\n`);
-                process.stderr.write(`  \x1b[32m✓\x1b[0m Credentials saved to ~/.atoms/credentials.json\n\n`);
-                process.stderr.write(`  \x1b[1mNext steps:\x1b[0m\n`);
-                process.stderr.write(`  \x1b[36m$\x1b[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(`  \x1b[90m{\n    "mcpServers": {\n      "atoms": {\n        "command": "npx",\n        "args": ["-y", "@atoms-tech/atoms-mcp"]\n      }\n    }\n  }\x1b[0m\n\n`);
-            }
-            catch (err) {
-                process.stderr.write(`\n  \x1b[31m✗\x1b[0m ${err instanceof Error ? err.message : String(err)}\n\n`);
-                process.exit(1);
-            }
-            break;
-        }
-        case "whoami": {
-            const { getValidToken } = await import("./auth/refresh.js");
-            try {
-                const { email, user_id } = await getValidToken();
-                process.stderr.write(`\n  \x1b[32m✓\x1b[0m Logged in as ${email}\n  \x1b[90mUser ID: ${user_id}\x1b[0m\n\n`);
-            }
-            catch (err) {
-                process.stderr.write(`\n  \x1b[31m✗\x1b[0m Not authenticated.\n  Run: npx @atoms-tech/atoms-mcp login\n\n`);
-                process.exit(1);
-            }
-            break;
-        }
-        case "logout": {
-            const { clearCredentials } = await import("./auth/token-store.js");
-            await clearCredentials();
-            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 v0.1.0\n");
-            break;
-        }
-        case "--help":
-        case "-h": {
-            process.stderr.write(`ATOMS MCP Server — AI agent integration for requirements management\n\n` +
-                `Usage:\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: {
-            // Default: start MCP server via stdio
-            process.stderr.write("[atoms-mcp] Starting MCP server via stdio...\n");
-            try {
-                // Validate auth on startup
-                const { getValidToken } = await import("./auth/refresh.js");
-                const { email } = await getValidToken();
-                process.stderr.write(`[atoms-mcp] Authenticated as ${email}\n`);
-            }
-            catch (err) {
-                process.stderr.write(`[atoms-mcp] Warning: ${err instanceof Error ? err.message : String(err)}\n` +
-                    `[atoms-mcp] Some tools may fail without authentication.\n`);
-            }
-            const transport = new StdioServerTransport();
-            await server.connect(transport);
-            process.stderr.write("[atoms-mcp] MCP server running. Waiting for tool calls...\n");
-        }
-    }
-}
-main().catch((err) => {
-    process.stderr.write(`[atoms-mcp] Fatal: ${err instanceof Error ? err.message : String(err)}\n`);
-    process.exit(1);
-});
+import e,{readFile as t,mkdir as r,writeFile as n,unlink as i}from"fs/promises";import{homedir as s}from"os";import a,{join as o}from"path";import{createClient as c}from"@supabase/supabase-js";import{registerAppTool as d,registerAppResource as l,RESOURCE_MIME_TYPE as m}from"@modelcontextprotocol/ext-apps/server";import{URL as p,fileURLToPath as u}from"url";import{McpServer as h}from"@modelcontextprotocol/sdk/server/mcp.js";import{z as _}from"zod";import{randomUUID as g,randomBytes as f,createHash as y}from"crypto";import{createServer as w}from"http";import{StdioServerTransport as b}from"@modelcontextprotocol/sdk/server/stdio.js";var v,j,x,S,I,k=Object.defineProperty,E=Object.getOwnPropertyNames,T=(e,t)=>function(){return e&&(t=(0,e[E(e)[0]])(e=0)),t},H=(e,t)=>{for(var r in t)k(e,r,{get:t[r],enumerable:!0})},C=T({"src/middleware/audit.ts"(){}}),O=T({"src/middleware/rate-limiter.ts"(){v=60,j=6e4,x=new Map}}),D={};async function U(){try{const e=await t(I,"utf-8"),r=JSON.parse(e);return r.access_token&&r.refresh_token?r:null}catch{return null}}async function M(e){await r(S,{recursive:!0,mode:448}),await n(I,JSON.stringify(e,null,2),{mode:384})}async function q(){const e=await U();return!!e&&e.expires_at>Date.now()+6e4}async function P(){try{await i(I)}catch{}}function A(){return I}H(D,{clearCredentials:()=>P,getCredentialsPath:()=>A,hasValidCredentials:()=>q,readCredentials:()=>U,writeCredentials:()=>M});var R,$,N,W=T({"src/auth/token-store.ts"(){S=o(s(),".atoms"),I=o(S,"credentials.json")}}),F=T({"src/config.ts"(){R="https://gmebjyhomsbvhrxffzre.supabase.co",$="sb_publishable_b49MUAB8XCrQiF7x5b9lUA_w1aplSBH",N=process.env.ATOMS_APP_URL??"https://x.atoms.tech"}}),L={};async function z(){const e=process.env.ATOMS_ACCESS_TOKEN;if(e){const t=J(e);return{access_token:e,refresh_token:"",user_id:t.sub,email:t.email??""}}const t=await U();if(!t)throw new Error("Not authenticated. Run 'npx @atoms-tech/atoms-mcp login' to connect your ATOMS account.");if(t.expires_at>Date.now()+6e4){const e=J(t.access_token);return{access_token:t.access_token,refresh_token:t.refresh_token,user_id:e.sub,email:e.email??t.user_email??""}}process.stderr.write("[atoms-mcp] Refreshing access token...\n");const r=c(R,$),{data:n,error:i}=await r.auth.refreshSession({refresh_token:t.refresh_token});if(i||!n.session)throw new Error(`Token refresh failed: ${i?.message??"No session returned"}. Re-run 'npx @atoms-tech/atoms-mcp login'.`);const s=n.session;return await M({access_token:s.access_token,refresh_token:s.refresh_token,expires_at:Date.now()+1e3*(s.expires_in??3600),user_email:s.user?.email}),{access_token:s.access_token,refresh_token:s.refresh_token,user_id:s.user?.id??"",email:s.user?.email??""}}function J(e){const t=e.split(".");if(3!==t.length)throw new Error("Invalid JWT format");const r=t[1].replace(/-/g,"+").replace(/_/g,"/").padEnd(t[1].length+(4-t[1].length%4)%4,"="),n=JSON.parse(Buffer.from(r,"base64").toString("utf-8"));if(!n.sub)throw new Error("JWT missing 'sub' claim");return n}H(L,{getValidToken:()=>z});var B,V,G,Q,Y=T({"src/auth/refresh.ts"(){W(),F()}});async function K(){if(B&&Q>Date.now()+6e4)return B;B&&process.stderr.write("[atoms-mcp] Token expiring, refreshing client...\n");const{access_token:e,user_id:t,email:r}=await z(),n=e.split(".");if(3===n.length)try{const e=JSON.parse(Buffer.from(n[1].replace(/-/g,"+").replace(/_/g,"/"),"base64").toString());Q=1e3*(e.exp??0)}catch{Q=Date.now()+36e5}const i=c(R,$,{global:{headers:{Authorization:`Bearer ${e}`}}});return V=t,G=r,B=i}function X(){if(!V)throw new Error("Not authenticated. Call getClient() first.");return V}async function Z(e,t){const r=X(),{data:n,error:i}=await e.from("projects").select("org_id").eq("id",t).maybeSingle();if(i||!n)throw new Error(`Project '${t}' not found`);const{data:s,error:a}=await e.from("org_members").select("role").eq("user_id",r).eq("org_id",n.org_id).maybeSingle();if(a||!s){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"===s.role)throw new Error("VIEWER_ROLE");return s.role}var ee,te=T({"src/db/client.ts"(){Y(),F(),B=null,V=null,G=null,Q=0}});function re(e,t){return{status:"success",data:e,...t?{meta:t}:{}}}function ne(e,t,r){return{total_count:e,limit:t,offset:r,has_more:r+t<e}}function ie(e,t){return{status:"error",message:e,next_steps:t}}function se(e,t){return ie(`${e} '${t}' not found`,[`Verify the ${e.toLowerCase()} ID is correct`,"Use atoms_list_items or atoms_search to find valid IDs"])}function ae(e){return ie(`${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 oe(e){return ie(`Validation error: ${e}`,["Check the parameter types and constraints in the tool description","Ensure all required parameters are provided"])}function ce(){return ie("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 de(e){return ie(`Database error: ${e}`,["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 ${t} items. Use 'offset' parameter or add filters to see more results.`}};return{content:[{type:"text",text:JSON.stringify(r,null,2)}],structuredContent:r}}return{content:[{type:"text",text:t}],structuredContent:e}}function me(e){return{content:[{type:"text",text:JSON.stringify(e,null,2)}],structuredContent:e,isError:!0}}var pe,ue=T({"src/tools/_base.ts"(){ee=25e3}});function he(t,r){const n=`ui://${r.toolName}/${r.htmlFile}`,i=function(e,t){const r=u(import.meta.url),n=a.dirname(r);return a.resolve(n,"apps","src","apps",e,t)}(r.appName,r.htmlFile),s=[...pe.resourceDomains,...r.extraResourceDomains??[]];d(t,r.toolName,{title:r.title,description:r.description,inputSchema:r.inputSchema,annotations:r.annotations,_meta:{ui:{resourceUri:n}}},r.handler),l(t,`${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:s}}}}]}})}var _e=T({"src/apps/register.ts"(){pe={resourceDomains:["fonts.googleapis.com","fonts.gstatic.com"]}}});async function ge(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 fe(e,t,r){const n="requirement"===r?"REQ":"test-case"===r?"TC":"note"===r?"NOTE":"TABLE",{data:i,error:s}=await e.rpc("next_item_id",{p_project_id:t,p_prefix:n});if(s)throw new Error(`ID generation failed: ${s.message}`);return i}var ye=T({"src/db/queries.ts"(){}}),we={};async function be(){try{const e=await K(),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 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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=s.map(t=>({item_id:t.id,project_id:e.project_id,changed_by:r,event_type:"created",old_data:null,new_data:d.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: ${e.message}\n`)}),le(re({created:s.length,items:s,errors:a.length>0?a:[],project_id:e.project_id}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?me(ce()):me(de(e instanceof Error?e.message:String(e)))}}H(Ze,{bulkImportHandler:()=>et});var tt=T({"src/tools/bulk-import.ts"(){te(),ye(),jt(),ue()}}),rt={};async function nt(e){try{const t=await K(),r=X(),n=G??"";try{await Z(t,e.project_id)}catch(e){if(e instanceof Error&&"VIEWER_ROLE"===e.message)return me(ae("Viewer"));throw e}const i=await ge(t,e.project_id,e.item_id);if(!i)return me(se("Item",e.item_id));if("test-case"!==i.type)return me(oe(`Item '${e.item_id}' is a ${i.type}, not a test-case`));const s=(new Date).toISOString(),{error:a}=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:s,note:e.note??null});if(a)throw new Error(a.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:s,note:e.note},actor:"mcp_claude",session_id:wt()}).then(({error:e})=>{e&&process.stderr.write(`[atoms-mcp] Warning: change_history log failed: ${e.message}\n`)}),le(re({item_id:e.item_id,result:e.result,run_at:s,run_by:n||r,note:e.note??null,message:`Test result '${e.result}' recorded for ${e.item_id}`}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?me(ce()):me(de(e instanceof Error?e.message:String(e)))}}H(rt,{recordTestResultHandler:()=>nt});var it,st,at,ot,ct=T({"src/tools/record-test-result.ts"(){te(),ye(),jt(),ue()}}),dt={};async function lt(e){try{const t=Math.min(Math.max(e.depth??5,1),10),r=await K();if(!await ge(r,e.project_id,e.item_id))return me(se("Item",e.item_id));const{data:n,error:i}=await r.from("item_relationships").select("from_id, to_id, type").eq("project_id",e.project_id);if(i)throw new Error(i.message);const{data:s,error:a}=await r.from("items").select("id, title, type").eq("project_id",e.project_id).is("deleted_at",null);if(a)throw new Error(a.message);const o=new Map;for(const e of s??[])o.set(e.id,{title:e.title,type:e.type});const c=new Map,d=(e,t,r)=>{c.has(e)||c.set(e,[]),c.get(e).push({neighbor:t,relType:r})},l=e.relationship_types?new Set(e.relationship_types):null;for(const t of n??[]){const r=t.type;if(("upstream"===e.direction||"both"===e.direction)&&(st.includes(r)&&(l&&!l.has(r)||d(t.from_id,t.to_id,r)),at.includes(r))){const e=ot[r]??r;l&&!l.has(e)||d(t.to_id,t.from_id,e)}if(("downstream"===e.direction||"both"===e.direction)&&(at.includes(r)&&(l&&!l.has(r)||d(t.from_id,t.to_id,r)),st.includes(r))){const e=ot[r]??r;l&&!l.has(e)||d(t.to_id,t.from_id,e)}"related"===r&&(l&&!l.has("related")||(d(t.from_id,t.to_id,"related"),d(t.to_id,t.from_id,"related")))}const m=new Set;m.add(e.item_id);const p=[],u=[],h=c.get(e.item_id)??[];for(const e of h)u.push({id:e.neighbor,depth:1,relType:e.relType});for(;u.length>0&&p.length<it;){const{id:e,depth:r,relType:n}=u.shift();if(m.has(e)||r>t)continue;m.add(e);const i=o.get(e);if(i&&(p.push({id:e,title:i.title,type:i.type,relationship:n,depth:r}),r<t)){const t=c.get(e)??[];for(const e of t)m.has(e.neighbor)||u.push({id:e.neighbor,depth:r+1,relType:e.relType})}}return le(re({root:e.item_id,direction:e.direction,depth_limit:t,items:p,total_count:p.length,...p.length>=it?{truncated:!0,truncation_message:`Results capped at ${it} items. Use a smaller depth or filter by relationship_types.`}:{}}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?me(ce()):me(de(e instanceof Error?e.message:String(e)))}}H(dt,{traceHandler:()=>lt});var mt=T({"src/tools/trace.ts"(){te(),ye(),ue(),it=200,st=["parent","verifies"],at=["child","verified_by"],ot={parent:"child",child:"parent",verifies:"verified_by",verified_by:"verifies",related:"related"}}}),pt={};async function ut(e){try{const t=await K(),{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 me(se("Project",e.project_id));const{data:i,error:s}=await t.from("items").select("id, type, data").eq("project_id",e.project_id).is("deleted_at",null);if(s)throw new Error(s.message);const a=i??[],o={requirements:0,test_cases:0,notes:0},c=[],d=[];for(const e of a)if("requirement"===e.type){o.requirements++;const t=e.data?.tags?.domains??[];d.push({id:e.id,domains:t})}else"test-case"===e.type?(o.test_cases++,c.push(e.id)):"note"===e.type&&o.notes++;const l={passed:0,failed:0,blocked:0,not_run:0};if(c.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 c){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)),h=d.filter(e=>u.has(e.id)).length,_=d.length,g={covered:h,uncovered:_-h,total:_,percent:_>0?Math.round(h/_*1e3)/10:100},f=new Map;for(const e of d){const t=e.domains.length>0?e.domains:["(untagged)"],r=u.has(e.id);for(const e of t){f.has(e)||f.set(e,{covered:0,total:0});const t=f.get(e);t.total++,r&&t.covered++}}const y=Array.from(f.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})),w=new Date;w.setDate(w.getDate()-7);const{count:b,error:v}=await t.from("change_history").select("id",{count:"exact",head:!0}).eq("project_id",e.project_id).gte("changed_at",w.toISOString());if(v)throw new Error(v.message);return le(re({project_id:e.project_id,project_name:r.name,counts:o,test_status:l,coverage:g,coverage_by_domain:y,recent_changes:b??0,last_updated:(new Date).toISOString()}))}catch(e){return e instanceof Error&&e.message.includes("Not authenticated")?me(ce()):me(de(e instanceof Error?e.message:String(e)))}}H(pt,{projectSummaryHandler:()=>ut});var ht,_t,gt,ft=T({"src/tools/project-summary.ts"(){te(),ue()}});function yt(e,t){return async r=>{let n;try{await K(),n=X()}catch{return t(r)}const i=function(e){const t=parseInt(process.env.ATOMS_RATE_LIMIT_RPM??"",10)||v,r=Date.now(),n=r-j;let i=x.get(e);if(i||(i={timestamps:[]},x.set(e,i)),i.timestamps=i.timestamps.filter(e=>e>n),i.timestamps.length>=t){const e=i.timestamps[0]+j-r;return{allowed:!1,retryAfterSeconds:Math.ceil(e/1e3)}}return i.timestamps.push(r),{allowed:!0}}(n);if(!i.allowed)return me(ie("Rate limit exceeded",[`Wait ${i.retryAfterSeconds} seconds before making more requests`,"Reduce the frequency of tool calls"]));const s=function(){const e=performance.now();return()=>Math.round(performance.now()-e)}();let a,o="success";try{const e=await t(r),n=e;if(!0===n?.isError){o="error";const e=n?.content;if(e?.[0]?.text)try{a=JSON.parse(e[0].text).message}catch{}}return e}catch(e){throw o="error",a=e instanceof Error?e.message:String(e),e}finally{const t={tool_name:e,params:r,status:o,duration_ms:s(),error_msg:a,project_id:r.project_id,session_id:_t,client_name:gt};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 K(),n,t)}catch{}}}}function wt(){return _t}var bt,vt,jt=T({"src/server.ts"(){C(),O(),te(),ue(),_e(),ht=new h({name:"atoms-mcp-server",version:"0.1.0"}),_t=g(),gt=process.env.ATOMS_CLIENT_NAME??"unknown",ht.registerTool("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}},yt("atoms_list_projects",async()=>{const{listProjectsHandler:e}=await Promise.resolve().then(()=>(ve(),we));return e()})),ht.registerTool("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:_.string().uuid("Must be a valid project UUID").describe("UUID of the project"),type:_.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),domain:_.string().optional().describe("Filter by domain tag (e.g., 'Safety', 'Performance')"),level:_.string().optional().describe("Filter by level (System, Subsystem, Component)"),limit:_.number().int().min(1).max(200).default(50).describe("Max results (default 50, max 200)"),offset:_.number().int().min(0).default(0).describe("Pagination offset (default 0)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},yt("atoms_list_items",async e=>{const{listItemsHandler:t}=await Promise.resolve().then(()=>(Se(),je));return t(e)})),ht.registerTool("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-00001", "TC-00050")\n\nReturns:\n  Full WorkItem with relationships, test runs, ownership, metadata.\n\nExamples:\n  - "Show me requirement REQ-00001" → atoms_get_item(project_id, "REQ-00001")\n  - "Get test case details" → atoms_get_item(project_id, "TC-00050")',inputSchema:{project_id:_.string().uuid().describe("UUID of the project"),item_id:_.string().min(1).max(20).describe("Item ID (e.g., REQ-00001)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},yt("atoms_get_item",async e=>{const{getItemHandler:t}=await Promise.resolve().then(()=>(Ee(),Ie));return t(e)})),ht.registerTool("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:_.string().uuid().describe("UUID of the project"),query:_.string().min(1).max(1e3).describe("Search text"),type:_.enum(["requirement","test-case","note","table"]).optional().describe("Filter by item type"),limit:_.number().int().min(1).max(100).default(25).describe("Max results (default 25, max 100)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},yt("atoms_search",async e=>{const{searchHandler:t}=await Promise.resolve().then(()=>(Ce(),Te));return t(e)})),he(ht,{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:_.string().uuid().describe("UUID of the project"),domain:_.string().optional().describe("Filter by domain tag"),level:_.string().optional().describe("Filter by level")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:yt("atoms_get_coverage",async e=>{const{getCoverageHandler:t}=await Promise.resolve().then(()=>(Ue(),Oe));return t(e)})}),ht.registerTool("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:_.string().uuid().describe("UUID of the project"),item_id:_.string().min(1).max(20).describe("Item ID"),limit:_.number().int().min(1).max(100).default(20).describe("Max entries (default 20)")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},yt("atoms_get_history",async e=>{const{getHistoryHandler:t}=await Promise.resolve().then(()=>(Pe(),Me));return t(e)})),he(ht,{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:_.string().uuid().describe("UUID of the project"),root_item_id:_.string().optional().describe("Root item ID to start from"),depth:_.number().int().min(1).max(10).default(3).describe("Max depth"),include_tests:_.boolean().default(!0).describe("Include test case links")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},extraResourceDomains:["cdn.jsdelivr.net"],handler:yt("atoms_export_mermaid",async e=>{const{exportMermaidHandler:t}=await Promise.resolve().then(()=>(Ne(),Ae));return t(e)})}),ht.registerTool("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-00058\")\n\nSide effects:\n  - Logs to change_history with actor='mcp_claude'\n  - Creates relationships if parent_ids provided",inputSchema:{project_id:_.string().uuid().describe("UUID of the target project"),type:_.enum(["requirement","test-case","note"]).describe("Item type"),title:_.string().min(1).max(500).describe("Item title"),body:_.string().optional().describe("Rich text body"),summary:_.string().optional().describe("Brief summary"),domains:_.array(_.string()).optional().describe("Domain tags"),level:_.string().optional().describe("System|Subsystem|Component"),parent_ids:_.array(_.string()).optional().describe("Parent item IDs to link")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},yt("atoms_create_item",async e=>{const{createItemHandler:t}=await Promise.resolve().then(()=>(Le(),We));return t(e)})),ht.registerTool("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:_.string().uuid().describe("UUID of the project"),item_id:_.string().min(1).max(20).describe("Item ID to update"),title:_.string().min(1).max(500).optional().describe("New title"),body:_.string().optional().describe("New body"),summary:_.string().optional().describe("New summary"),domains:_.array(_.string()).optional().describe("New domain tags"),level:_.string().optional().describe("New level"),status:_.enum(["passed","failed","blocked","not-run"]).optional().describe("Test case status")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},yt("atoms_update_item",async e=>{const{updateItemHandler:t}=await Promise.resolve().then(()=>(Be(),ze));return t(e)})),ht.registerTool("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\nArgs:\n  - project_id (string, UUID): Project containing the item\n  - item_id (string): Item to delete\n\nReturns:\n  Confirmation with deleted item summary.",inputSchema:{project_id:_.string().uuid().describe("UUID of the project"),item_id:_.string().min(1).max(20).describe("Item ID to soft-delete")},annotations:{readOnlyHint:!1,destructiveHint:!0,idempotentHint:!0,openWorldHint:!1}},yt("atoms_delete_item",async e=>{const{deleteItemHandler:t}=await Promise.resolve().then(()=>(Qe(),Ve));return t(e)})),ht.registerTool("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:_.string().uuid().describe("UUID of the project"),from_id:_.string().min(1).max(20).describe("Source item ID"),to_id:_.string().min(1).max(20).describe("Target item ID"),type:_.enum(["parent","child","related","verifies","verified_by"]).describe("Relationship type"),action:_.enum(["add","remove"]).describe("Add or remove the relationship")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1}},yt("atoms_link_items",async e=>{const{linkItemsHandler:t}=await Promise.resolve().then(()=>(Xe(),Ye));return t(e)})),he(ht,{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:_.string().uuid().describe("UUID of the target project"),items:_.array(_.object({type:_.enum(["requirement","test-case","note"]).describe("Item type"),title:_.string().min(1).max(500).describe("Item title"),body:_.string().optional().describe("Rich text body"),summary:_.string().optional().describe("Brief summary"),domains:_.array(_.string()).optional().describe("Domain tags"),level:_.string().optional().describe("System|Subsystem|Component"),parent_id:_.string().optional().describe("Parent item ID to link")})).min(1).max(100).describe("Items to create (1-100)")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1},handler:yt("atoms_bulk_import",async e=>{const{bulkImportHandler:t}=await Promise.resolve().then(()=>(tt(),Ze));return t(e)})}),ht.registerTool("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-00001\")\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:_.string().uuid().describe("UUID of the project"),item_id:_.string().min(1).max(20).describe("Test case ID (e.g., TC-00001)"),result:_.enum(["passed","failed","blocked","not-run"]).describe("Test result"),note:_.string().max(1e3).optional().describe("Reason or comment for this result")},annotations:{readOnlyHint:!1,destructiveHint:!1,idempotentHint:!1,openWorldHint:!1}},yt("atoms_record_test_result",async e=>{const{recordTestResultHandler:t}=await Promise.resolve().then(()=>(ct(),rt));return t(e)})),he(ht,{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-00003 verify?" or\n"if I change REQ-00001, 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-00003 verify?" → atoms_trace(project_id, "TC-00003", "upstream")\n  - "What\'s affected by REQ-00001?" → atoms_trace(project_id, "REQ-00001", "downstream")',inputSchema:{project_id:_.string().uuid().describe("UUID of the project"),item_id:_.string().min(1).max(20).describe("Starting item ID"),direction:_.enum(["upstream","downstream","both"]).describe("Traversal direction"),depth:_.number().int().min(1).max(10).default(5).describe("Max traversal depth (default 5)"),relationship_types:_.array(_.enum(["parent","child","related","verifies","verified_by"])).optional().describe("Filter to specific relationship types")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:yt("atoms_trace",async e=>{const{traceHandler:t}=await Promise.resolve().then(()=>(mt(),dt));return t(e)})}),he(ht,{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:_.string().uuid().describe("UUID of the project")},annotations:{readOnlyHint:!0,destructiveHint:!1,idempotentHint:!0,openWorldHint:!1},handler:yt("atoms_project_summary",async e=>{const{projectSummaryHandler:t}=await Promise.resolve().then(()=>(ft(),pt));return t(e)})})}}),xt={};async function St(){const e=f(32).toString("base64url"),t=y("sha256").update(e).digest("base64url"),r=`http://localhost:${bt}${vt}`,n=new p(`${N}/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)=>{const i=w(async(n,s)=>{const a=new p(n.url??"/",`http://localhost:${bt}`);if(a.pathname!==vt)return s.writeHead(404),void s.end("Not found");try{if("access_denied"===a.searchParams.get("error"))return s.writeHead(200,{"Content-Type":"text/html"}),s.end(kt("Authorization was cancelled.")),i.close(),void r(new Error("Authorization cancelled by user."));const n=a.searchParams.get("code");if(n){const a=await fetch(`${R}/auth/v1/token?grant_type=pkce`,{method:"POST",headers:{"Content-Type":"application/json",apikey:$},body:JSON.stringify({auth_code:n,code_verifier:e})}),o=await a.json();if(!a.ok||!o.access_token){const e=o.error_description??o.msg??"Unknown error";return s.writeHead(200,{"Content-Type":"text/html"}),s.end(kt(`Code exchange failed: ${e}`)),i.close(),void r(new Error(`Code exchange failed: ${e}`))}let c="authenticated";try{c=JSON.parse(Buffer.from(o.access_token.split(".")[1],"base64").toString()).email??c}catch{}const{createClient:d}=await import("@supabase/supabase-js"),l=d(R,$,{global:{headers:{Authorization:`Bearer ${o.access_token}`}}}),{data:m,error:p}=await l.from("org_members").select("org_id").limit(1);return p||!m||0===m.length?(s.writeHead(200,{"Content-Type":"text/html"}),s.end(kt('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.')),i.close(),void r(new Error("No ATOMS account found. Sign up at x.atoms.tech first."))):(await M({access_token:o.access_token,refresh_token:o.refresh_token,expires_at:Date.now()+1e3*(o.expires_in??3600),user_email:c}),s.writeHead(200,{"Content-Type":"text/html"}),s.end(It(c)),i.close(),void t({email:c}))}const o=a.searchParams.get("access_token"),c=a.searchParams.get("refresh_token"),d=parseInt(a.searchParams.get("expires_in")??"3600",10);o&&c?(await M({access_token:o,refresh_token:c,expires_at:Date.now()+1e3*d}),s.writeHead(200,{"Content-Type":"text/html"}),s.end(It("authenticated")),i.close(),t({email:"authenticated"})):(s.writeHead(200,{"Content-Type":"text/html"}),s.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){s.writeHead(500),s.end("Authentication failed"),i.close(),r(e)}});i.on("request",async(e,n)=>{if("POST"===e.method&&"/token"===e.url){let s="";e.on("data",e=>{s+=e.toString()}),e.on("end",async()=>{try{const e=JSON.parse(s);await M({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})),i.close(),t({email:e.user_email??"authenticated"})}catch(e){n.writeHead(500),n.end("Failed to store credentials"),i.close(),r(e)}})}}),i.listen(bt,"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")}}),setTimeout(()=>{i.close(),r(new Error("Login timed out after 5 minutes"))},3e5)})}function It(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 kt(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>`}H(xt,{login:()=>St});var Et=T({"src/auth/login.ts"(){W(),F(),bt=19275,vt="/callback"}});jt();var Tt=process.argv.slice(2)[0];(async function(){switch(Tt){case"login":{const{login:e}=await Promise.resolve().then(()=>(Et(),xt));try{const{email:t}=await e();process.stderr.write(`\n  ✓ Authenticated as ${t}\n`),process.stderr.write("  ✓ Credentials saved to ~/.atoms/credentials.json\n\n"),process.stderr.write("  Next steps:\n"),process.stderr.write("  $ claude mcp add atoms -- npx -y @atoms-tech/atoms-mcp\n"),process.stderr.write("\n  Or add to Claude Desktop (Settings → MCP → Edit Config):\n"),process.stderr.write('  {\n    "mcpServers": {\n      "atoms": {\n        "command": "npx",\n        "args": ["-y", "@atoms-tech/atoms-mcp"]\n      }\n    }\n  }\n\n')}catch(e){process.stderr.write(`\n  ✗ ${e instanceof Error?e.message:String(e)}\n\n`),process.exit(1)}break}case"whoami":{const{getValidToken:e}=await Promise.resolve().then(()=>(Y(),L));try{const{email:t,user_id:r}=await e();process.stderr.write(`\n  ✓ Logged in as ${t}\n  User ID: ${r}\n\n`)}catch(e){process.stderr.write("\n  ✗ Not authenticated.\n  Run: npx @atoms-tech/atoms-mcp login\n\n"),process.exit(1)}break}case"logout":{const{clearCredentials:e}=await Promise.resolve().then(()=>(W(),D));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 v0.1.0\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(()=>(Y(),L)),{email:t}=await e();process.stderr.write(`[atoms-mcp] Authenticated as ${t}\n`)}catch(e){process.stderr.write(`[atoms-mcp] Warning: ${e instanceof Error?e.message:String(e)}\n[atoms-mcp] Some tools may fail without authentication.\n`)}const e=new b;await ht.connect(e),process.stderr.write("[atoms-mcp] MCP server running. Waiting for tool calls...\n")}}})().catch(e=>{process.stderr.write(`[atoms-mcp] Fatal: ${e instanceof Error?e.message:String(e)}\n`),process.exit(1)});

package/package.json

@@ -1,15 +1,22 @@
 {
   "name": "@atoms-tech/atoms-mcp",
-  "version": "0.3.0",
+  "version": "0.3.1",
   "description": "MCP server for ATOMS.tech — AI agent integration for requirements management",
   "type": "module",
-  "main": "dist/index.js",
+  "main": "dist/index.cjs",
+  "module": "dist/index.js",
+  "exports": {
+    ".": {
+      "import": "./dist/index.js",
+      "require": "./dist/index.cjs"
+    }
+  },
   "bin": {
     "atoms-mcp": "./bin/atoms-mcp.js"
   },
   "scripts": {
     "build:ui": "rm -rf dist/apps && INPUT=src/apps/mermaid/mermaid-app.html vite build && INPUT=src/apps/summary/summary-app.html vite build && INPUT=src/apps/trace/trace-app.html vite build && INPUT=src/apps/coverage/coverage-app.html vite build && INPUT=src/apps/import/import-app.html vite build",
-    "build:server": "tsc",
+    "build:server": "tsup",
     "build": "npm run build:ui && npm run build:server",
     "dev": "tsx watch src/index.ts",
     "dev:ui": "vite build --watch",
@@ -32,6 +39,8 @@
   },
   "devDependencies": {
     "@types/node": "^22.0.0",
+    "terser": "^5.46.1",
+    "tsup": "^8.5.1",
     "tsx": "^4.19.0",
     "typescript": "^5.9.0",
     "vite": "^7.3.1",

package/dist/apps/register.d.ts

@@ -1,36 +0,0 @@
-/**
- * MCP App registration helper.
- * Wraps registerAppTool + registerAppResource with ATOMS conventions.
- */
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import type { ToolAnnotations } from "@modelcontextprotocol/sdk/types.js";
-import type { ZodRawShapeCompat } from "@modelcontextprotocol/sdk/server/zod-compat.js";
-interface RegisterAppConfig {
-    /** App directory name (e.g., "mermaid") */
-    appName: string;
-    /** HTML filename (e.g., "mermaid-app.html") */
-    htmlFile: string;
-    /** Tool name (e.g., "atoms_export_mermaid") */
-    toolName: string;
-    /** Tool display title */
-    title: string;
-    /** Tool description */
-    description: string;
-    /** Zod input schema */
-    inputSchema: ZodRawShapeCompat;
-    /** Tool annotations */
-    annotations?: ToolAnnotations;
-    /** Additional CSP resource domains (e.g., CDN for mermaid.js) */
-    extraResourceDomains?: string[];
-    /** Tool handler — receives validated params, returns MCP tool result */
-    handler: (...args: any[]) => any;
-}
-/**
- * Register a tool as an MCP App with UI resource.
- * - Creates ui:// resource URI
- * - Registers tool with _meta.ui pointing to the resource
- * - Registers resource that serves the single-file bundled HTML
- * - Configures CSP for Google Fonts + any extras
- */
-export declare function registerAtomsApp(server: McpServer, config: RegisterAppConfig): void;
-export {};

package/dist/apps/register.js

@@ -1,65 +0,0 @@
-/**
- * MCP App registration helper.
- * Wraps registerAppTool + registerAppResource with ATOMS conventions.
- */
-import { registerAppTool, registerAppResource, RESOURCE_MIME_TYPE, } from "@modelcontextprotocol/ext-apps/server";
-import fs from "node:fs/promises";
-import path from "node:path";
-import { fileURLToPath } from "node:url";
-const __dirname = path.dirname(fileURLToPath(import.meta.url));
-/**
- * Resolve path to a built MCP App HTML file.
- * Build output: dist/apps/src/apps/{name}/{name}-app.html
- * Runtime __dirname: dist/apps/ (since this file is src/apps/register.ts → dist/apps/register.js)
- */
-function resolveAppHtml(appName, htmlFile) {
-    return path.resolve(__dirname, "src", "apps", appName, htmlFile);
-}
-/** CSP domains needed by all ATOMS apps (Google Fonts) */
-const SHARED_CSP = {
-    resourceDomains: [
-        "fonts.googleapis.com",
-        "fonts.gstatic.com",
-    ],
-};
-/**
- * Register a tool as an MCP App with UI resource.
- * - Creates ui:// resource URI
- * - Registers tool with _meta.ui pointing to the resource
- * - Registers resource that serves the single-file bundled HTML
- * - Configures CSP for Google Fonts + any extras
- */
-export function registerAtomsApp(server, config) {
-    const resourceUri = `ui://${config.toolName}/${config.htmlFile}`;
-    const htmlPath = resolveAppHtml(config.appName, config.htmlFile);
-    const resourceDomains = [
-        ...SHARED_CSP.resourceDomains,
-        ...(config.extraResourceDomains ?? []),
-    ];
-    // Register the tool with UI metadata
-    registerAppTool(server, config.toolName, {
-        title: config.title,
-        description: config.description,
-        inputSchema: config.inputSchema,
-        annotations: config.annotations,
-        _meta: { ui: { resourceUri } },
-    }, config.handler);
-    // Register the HTML resource
-    registerAppResource(server, `${config.title} UI`, resourceUri, {
-        mimeType: RESOURCE_MIME_TYPE,
-    }, async () => {
-        const html = await fs.readFile(htmlPath, "utf-8");
-        return {
-            contents: [{
-                    uri: resourceUri,
-                    mimeType: RESOURCE_MIME_TYPE,
-                    text: html,
-                    _meta: {
-                        ui: {
-                            csp: { resourceDomains },
-                        },
-                    },
-                }],
-        };
-    });
-}

package/dist/auth/login.d.ts

@@ -1,24 +0,0 @@
-/**
- * OAuth 2.1 PKCE login flow for the MCP CLI.
- *
- * Flow:
- * 1. Generate PKCE code_verifier + code_challenge
- * 2. Start HTTP server on localhost:19275
- * 3. Open browser to x.atoms.tech/auth/mcp-login (or Supabase auth directly)
- * 4. User authenticates → redirect to localhost with tokens
- * 5. Store tokens in ~/.atoms/credentials.json
- */
-/**
- * Run the interactive login flow.
- * Opens browser, waits for callback, stores tokens.
- *
- * Uses OAuth 2.1 PKCE flow with hosted consent page:
- * 1. Open browser to ATOMS consent page with code_challenge
- * 2. User reviews permissions and clicks "Authorize"
- * 3. Consent page redirects to Supabase OAuth with PKCE params
- * 4. Supabase returns authorization code to localhost callback
- * 5. Exchange code + code_verifier for session tokens
- */
-export declare function login(): Promise<{
-    email: string;
-}>;