@atoms-tech/atoms-mcp 0.1.1 → 0.2.1

package/README.md

@@ -0,0 +1,136 @@
+# @atoms-tech/atoms-mcp
+
+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)
+
+## Quick Start
+
+```bash
+# 1. Login to your ATOMS account
+npx @atoms-tech/atoms-mcp login
+
+# 2. Add to Claude Code
+claude mcp add atoms-mcp -- npx @atoms-tech/atoms-mcp
+```
+
+That's it. Claude can now read, create, and manage requirements in your ATOMS projects.
+
+## What It Does
+
+ATOMS MCP gives AI agents direct access to your requirements, test cases, and traceability data through the [Model Context Protocol](https://modelcontextprotocol.io). Agents can:
+
+- Browse projects, search requirements, and inspect items
+- Create and update requirements, test cases, and notes
+- Bulk import 100 items at a time
+- Link items with parent/child and verification relationships
+- Record test results and check coverage gaps
+- Export traceability diagrams as Mermaid graphs
+
+Every action is logged with AI actor attribution (`mcp_claude`) and enforces your organization's role-based permissions.
+
+## Available Tools
+
+| Tool | Description | Access |
+|------|-------------|--------|
+| `atoms_list_projects` | List all accessible projects | Read |
+| `atoms_list_items` | Browse items with type/domain/level filters | Read |
+| `atoms_get_item` | Get full item details with relationships | Read |
+| `atoms_search` | Full-text search across items | Read |
+| `atoms_get_coverage` | Find requirements without test cases | Read |
+| `atoms_get_history` | Audit trail for an item | Read |
+| `atoms_export_mermaid` | Generate traceability diagram | Read |
+| `atoms_create_item` | Create a requirement, test case, or note | Write |
+| `atoms_update_item` | Update item fields | Write |
+| `atoms_delete_item` | Soft-delete an item | Write |
+| `atoms_link_items` | Add/remove relationships between items | Write |
+| `atoms_bulk_import` | Bulk create up to 100 items at once | Write |
+| `atoms_record_test_result` | Record pass/fail for a test case | Write |
+| `atoms_trace` | Walk traceability graph (upstream/downstream) | Read |
+| `atoms_project_summary` | Project compliance dashboard (counts, coverage, status) | Read |
+
+## Authentication
+
+ATOMS MCP uses **OAuth 2.1 with PKCE** — the same flow used by GitHub CLI and Supabase CLI.
+
+```bash
+# Interactive login (opens browser)
+npx @atoms-tech/atoms-mcp login
+
+# Check current session
+npx @atoms-tech/atoms-mcp whoami
+
+# Clear credentials
+npx @atoms-tech/atoms-mcp logout
+```
+
+**How it works:**
+
+1. `login` opens your browser to the ATOMS consent page
+2. You approve the MCP connection with your ATOMS account
+3. Tokens are stored locally at `~/.atoms-mcp/credentials.json`
+4. Tokens auto-refresh — you only need to login once
+
+You can also set `ATOMS_ACCESS_TOKEN` as an environment variable for CI/headless use.
+
+## CLI Commands
+
+```
+npx @atoms-tech/atoms-mcp login     # Authenticate with ATOMS
+npx @atoms-tech/atoms-mcp logout    # Clear stored credentials
+npx @atoms-tech/atoms-mcp whoami    # Show current user
+npx @atoms-tech/atoms-mcp --help    # Show all commands
+```
+
+Running without a subcommand starts the MCP server on stdio.
+
+## Setup
+
+### Claude Code
+
+```bash
+claude mcp add atoms-mcp -- npx @atoms-tech/atoms-mcp
+```
+
+### Claude Desktop
+
+Add to your `claude_desktop_config.json`:
+
+```json
+{
+  "mcpServers": {
+    "atoms-mcp": {
+      "command": "npx",
+      "args": ["@atoms-tech/atoms-mcp"]
+    }
+  }
+}
+```
+
+### Cursor / Windsurf
+
+Add to your MCP configuration with `command: "npx"` and `args: ["@atoms-tech/atoms-mcp"]`. Refer to your editor's MCP documentation for the exact config file location.
+
+## Security
+
+- **Row Level Security (RLS)** — All queries run with the user's JWT. The server never uses a service role key. You can only access projects your organization has granted you access to.
+- **Role enforcement** — Write tools check your org role (viewer, editor, admin) before making changes. Viewers are blocked from mutations.
+- **Audit logging** — Every tool call is logged with tool name, parameters, duration, and session ID. Write operations log to `change_history` with `actor: "mcp_claude"`.
+- **Rate limiting** — Built-in per-user rate limiter prevents abuse.
+- **No secrets in the package** — The Supabase anon key is a publishable client key (like a Firebase API key). It grants zero data access without a valid user JWT.
+
+## Requirements
+
+- Node.js >= 18
+- An [ATOMS.tech](https://atoms.tech) account with at least one project
+
+## Links
+
+- [ATOMS.tech](https://atoms.tech) — Requirements management platform
+- [Model Context Protocol](https://modelcontextprotocol.io) — Open standard for AI tool integration
+- [GitHub](https://github.com/support-atoms-tech/atoms-mvp-v2) — Source code
+
+## License
+
+MIT

package/dist/auth/login.d.ts

@@ -12,10 +12,12 @@
  * Run the interactive login flow.
  * Opens browser, waits for callback, stores tokens.
  *
- * Uses OAuth 2.1 PKCE flow:
- * 1. Redirect to Supabase with code_challenge
- * 2. Supabase returns authorization code to localhost callback
- * 3. Exchange code + code_verifier for session 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;

package/dist/auth/login.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"login.d.ts","sourceRoot":"","sources":["../../src/auth/login.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAWH;;;;;;;;;;GAUG;AACH,wBAAsB,KAAK,IAAI,OAAO,CAAC;IAAE,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC,CAkMxD"}

package/dist/auth/login.js

@@ -12,17 +12,19 @@ import { createServer } from "node:http";
 import { randomBytes, createHash } from "node:crypto";
 import { URL } from "node:url";
 import { writeCredentials } from "./token-store.js";
-import { ATOMS_SUPABASE_URL, ATOMS_SUPABASE_ANON_KEY } from "../config.js";
+import { ATOMS_SUPABASE_URL, ATOMS_SUPABASE_ANON_KEY, ATOMS_APP_URL } from "../config.js";
 const CALLBACK_PORT = 19275;
 const CALLBACK_PATH = "/callback";
 /**
  * Run the interactive login flow.
  * Opens browser, waits for callback, stores tokens.
  *
- * Uses OAuth 2.1 PKCE flow:
- * 1. Redirect to Supabase with code_challenge
- * 2. Supabase returns authorization code to localhost callback
- * 3. Exchange code + code_verifier for session 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 async function login() {
     // Generate PKCE challenge
@@ -31,10 +33,9 @@ export async function login() {
         .update(codeVerifier)
         .digest("base64url");
     const redirectTo = `http://localhost:${CALLBACK_PORT}${CALLBACK_PATH}`;
-    // Build auth URL
-    const authUrl = new URL(`${ATOMS_SUPABASE_URL}/auth/v1/authorize`);
-    authUrl.searchParams.set("provider", "google");
-    authUrl.searchParams.set("redirect_to", redirectTo);
+    // Build consent page URL — hosted on ATOMS web app
+    const authUrl = new URL(`${ATOMS_APP_URL}/auth/mcp-consent`);
+    authUrl.searchParams.set("redirect_uri", redirectTo);
     authUrl.searchParams.set("code_challenge", codeChallenge);
     authUrl.searchParams.set("code_challenge_method", "S256");
     return new Promise((resolve, reject) => {
@@ -46,6 +47,15 @@ export async function login() {
                 return;
             }
             try {
+                // Check for user cancellation from consent page
+                const error = url.searchParams.get("error");
+                if (error === "access_denied") {
+                    res.writeHead(200, { "Content-Type": "text/html" });
+                    res.end(failurePage("Authorization was cancelled."));
+                    server.close();
+                    reject(new Error("Authorization cancelled by user."));
+                    return;
+                }
                 // PKCE flow: Supabase redirects with ?code=xxx in query params
                 const code = url.searchParams.get("code");
                 if (code) {

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package/dist/config.d.ts

@@ -14,4 +14,6 @@
  */
 export declare const ATOMS_SUPABASE_URL = "https://gmebjyhomsbvhrxffzre.supabase.co";
 export declare const ATOMS_SUPABASE_ANON_KEY = "sb_publishable_b49MUAB8XCrQiF7x5b9lUA_w1aplSBH";
+/** ATOMS web app URL — hosts the MCP consent page */
+export declare const ATOMS_APP_URL: string;
 //# sourceMappingURL=config.d.ts.map

package/dist/config.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,eAAO,MAAM,kBAAkB,6CAA6C,CAAC;AAC7E,eAAO,MAAM,uBAAuB,mDACc,CAAC"}
+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,eAAO,MAAM,kBAAkB,6CAA6C,CAAC;AAC7E,eAAO,MAAM,uBAAuB,mDACc,CAAC;AAEnD,qDAAqD;AACrD,eAAO,MAAM,aAAa,QAAsD,CAAC"}

package/dist/config.js

@@ -14,4 +14,6 @@
  */
 export const ATOMS_SUPABASE_URL = "https://gmebjyhomsbvhrxffzre.supabase.co";
 export const ATOMS_SUPABASE_ANON_KEY = "sb_publishable_b49MUAB8XCrQiF7x5b9lUA_w1aplSBH";
+/** ATOMS web app URL — hosts the MCP consent page */
+export const ATOMS_APP_URL = process.env.ATOMS_APP_URL ?? "https://x.atoms.tech";
 //# sourceMappingURL=config.js.map

package/dist/config.js.map

@@ -1 +1 @@
-{"version":3,"file":"config.js","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,0CAA0C,CAAC;AAC7E,MAAM,CAAC,MAAM,uBAAuB,GAClC,gDAAgD,CAAC"}
+{"version":3,"file":"config.js","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,0CAA0C,CAAC;AAC7E,MAAM,CAAC,MAAM,uBAAuB,GAClC,gDAAgD,CAAC;AAEnD,qDAAqD;AACrD,MAAM,CAAC,MAAM,aAAa,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,IAAI,sBAAsB,CAAC"}

package/dist/server.js

@@ -472,6 +472,57 @@ Returns:
     const { linkItemsHandler } = await import("./tools/link-items.js");
     return linkItemsHandler(params);
 }));
+server.registerTool("atoms_bulk_import", {
+    title: "Bulk Import ATOMS Items",
+    description: `Bulk create multiple items in a single tool call. Essential for AI agents
+that generate 20+ requirements at once.
+
+Checks write access once, generates sequential IDs, batch inserts all items,
+and reports per-item errors without aborting the entire batch.
+
+Args:
+  - project_id (string, UUID): Target project
+  - items (array): Up to 100 items to create, each with:
+    - type (string): requirement|test-case|note
+    - title (string): Item title (max 500 chars)
+    - body (string, optional): Rich text body
+    - summary (string, optional): Brief summary
+    - domains (string[], optional): Domain tags
+    - level (string, optional): System|Subsystem|Component
+    - parent_id (string, optional): Parent item ID to link
+
+Returns:
+  { created: number, items: [{ id, title, type }], errors: [] }
+
+Limits:
+  - Maximum 100 items per call
+  - If any item fails, others still succeed — errors reported separately
+
+Side effects:
+  - Logs to change_history with actor='mcp_claude' for each created item
+  - Creates parent relationships for items with parent_id`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the target project"),
+        items: z.array(z.object({
+            type: z.enum(["requirement", "test-case", "note"]).describe("Item type"),
+            title: z.string().min(1).max(500).describe("Item title"),
+            body: z.string().optional().describe("Rich text body"),
+            summary: z.string().optional().describe("Brief summary"),
+            domains: z.array(z.string()).optional().describe("Domain tags"),
+            level: z.string().optional().describe("System|Subsystem|Component"),
+            parent_id: z.string().optional().describe("Parent item ID to link"),
+        })).min(1).max(100).describe("Items to create (1-100)"),
+    },
+    annotations: {
+        readOnlyHint: false,
+        destructiveHint: false,
+        idempotentHint: false,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_bulk_import", async (params) => {
+    const { bulkImportHandler } = await import("./tools/bulk-import.js");
+    return bulkImportHandler(params);
+}));
 server.registerTool("atoms_record_test_result", {
     title: "Record Test Result",
     description: `Record a pass/fail/blocked result for a test case.
@@ -508,4 +559,79 @@ Side effects:
     const { recordTestResultHandler } = await import("./tools/record-test-result.js");
     return recordTestResultHandler(params);
 }));
+// ---------------------------------------------------------------------------
+// Tool Registration — Phase 4 (Advanced Tools)
+// ---------------------------------------------------------------------------
+server.registerTool("atoms_trace", {
+    title: "Trace Item Relationships",
+    description: `Walk the traceability graph from a starting item.
+
+Answers questions like "which requirements does TC-00003 verify?" or
+"if I change REQ-00001, what's affected downstream?"
+
+Args:
+  - project_id (string, UUID): Project containing the item
+  - item_id (string): Starting item ID
+  - direction (string): upstream|downstream|both
+    - upstream: follow parent/verifies links (dependencies)
+    - downstream: follow child/verified_by links (dependents)
+    - both: trace in both directions
+  - depth (number, optional): Max traversal depth (default 5, max 10)
+  - relationship_types (string[], optional): Filter to specific types (parent, child, related, verifies, verified_by)
+
+Returns:
+  { root, direction, items: [{ id, title, type, relationship, depth }], total_count }
+
+Examples:
+  - "What does TC-00003 verify?" → atoms_trace(project_id, "TC-00003", "upstream")
+  - "What's affected by REQ-00001?" → atoms_trace(project_id, "REQ-00001", "downstream")`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+        item_id: z.string().min(1).max(20).describe("Starting item ID"),
+        direction: z.enum(["upstream", "downstream", "both"])
+            .describe("Traversal direction"),
+        depth: z.number().int().min(1).max(10).default(5)
+            .describe("Max traversal depth (default 5)"),
+        relationship_types: z.array(z.enum(["parent", "child", "related", "verifies", "verified_by"])).optional()
+            .describe("Filter to specific relationship types"),
+    },
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_trace", async (params) => {
+    const { traceHandler } = await import("./tools/trace.js");
+    return traceHandler(params);
+}));
+server.registerTool("atoms_project_summary", {
+    title: "Project Compliance Summary",
+    description: `One-call project health and compliance dashboard.
+
+Returns item counts by type, test execution status, requirement coverage
+(overall and by domain), and recent change activity.
+
+Args:
+  - project_id (string, UUID): Project to summarize
+
+Returns:
+  { project_name, counts, test_status, coverage, coverage_by_domain, recent_changes, last_updated }
+
+Examples:
+  - "Give me a compliance snapshot" → atoms_project_summary(project_id)
+  - "How's our test coverage?" → atoms_project_summary(project_id)`,
+    inputSchema: {
+        project_id: z.string().uuid().describe("UUID of the project"),
+    },
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: false,
+    },
+}, withMiddleware("atoms_project_summary", async (params) => {
+    const { projectSummaryHandler } = await import("./tools/project-summary.js");
+    return projectSummaryHandler(params);
+}));
 //# sourceMappingURL=server.js.map

package/dist/server.js.map

@@ -1 +1 @@
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package/dist/tools/bulk-import.d.ts

@@ -0,0 +1,70 @@
+/**
+ * atoms_bulk_import — Bulk create multiple items in a single tool call.
+ * Essential for AI agents that generate 20+ requirements at once.
+ *
+ * Checks write access once, generates sequential IDs, batch inserts,
+ * and reports per-item errors without aborting the entire batch.
+ */
+interface BulkImportItem {
+    type: "requirement" | "test-case" | "note";
+    title: string;
+    body?: string;
+    summary?: string;
+    domains?: string[];
+    level?: string;
+    parent_id?: string;
+}
+interface CreatedItem {
+    id: string;
+    title: string;
+    type: string;
+}
+interface BulkImportError {
+    index: number;
+    title: string;
+    error: string;
+}
+export declare function bulkImportHandler(params: {
+    project_id: string;
+    items: BulkImportItem[];
+}): Promise<{
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    structuredContent: {
+        data: any[];
+        meta: {
+            truncated: boolean;
+            truncation_message: string;
+            total_count?: number | undefined;
+            limit?: number | undefined;
+            offset?: number | undefined;
+            has_more?: boolean | undefined;
+        };
+        status: "success";
+    };
+} | {
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    structuredContent: import("../types/responses.js").ToolError | import("../types/responses.js").ToolSuccess<{
+        created: number;
+        items: never[];
+        errors: BulkImportError[];
+    }>;
+} | {
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    structuredContent: import("../types/responses.js").ToolError | import("../types/responses.js").ToolSuccess<{
+        created: number;
+        items: CreatedItem[];
+        errors: BulkImportError[];
+        project_id: string;
+    }>;
+}>;
+export {};
+//# sourceMappingURL=bulk-import.d.ts.map

package/dist/tools/bulk-import.d.ts.map

@@ -0,0 +1 @@
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package/dist/tools/bulk-import.js

@@ -0,0 +1,188 @@
+/**
+ * atoms_bulk_import — Bulk create multiple items in a single tool call.
+ * Essential for AI agents that generate 20+ requirements at once.
+ *
+ * Checks write access once, generates sequential IDs, batch inserts,
+ * and reports per-item errors without aborting the entire batch.
+ */
+import { getClient, getUserId, requireWriteAccess } from "../db/client.js";
+import { generateItemId } from "../db/queries.js";
+import { getMcpSessionId } from "../server.js";
+import { formatToolResult, formatErrorResult, success, accessDeniedError, validationError, dbError, authError, } from "./_base.js";
+export async function bulkImportHandler(params) {
+    try {
+        // Validate item count
+        if (!params.items || params.items.length === 0) {
+            return formatErrorResult(validationError("items array must contain at least 1 item"));
+        }
+        if (params.items.length > 100) {
+            return formatErrorResult(validationError(`Maximum 100 items per call (received ${params.items.length}). Split into multiple calls.`));
+        }
+        const client = await getClient();
+        const userId = getUserId();
+        // Check write access once for the entire batch
+        try {
+            await requireWriteAccess(client, params.project_id);
+        }
+        catch (err) {
+            if (err instanceof Error && err.message === "VIEWER_ROLE") {
+                return formatErrorResult(accessDeniedError("Viewer"));
+            }
+            throw err;
+        }
+        const now = new Date().toISOString();
+        const sessionId = getMcpSessionId();
+        const created = [];
+        const errors = [];
+        // Generate all IDs sequentially (each call increments the counter)
+        const itemsWithIds = [];
+        for (let i = 0; i < params.items.length; i++) {
+            const input = params.items[i];
+            try {
+                const itemId = await generateItemId(client, params.project_id, input.type);
+                itemsWithIds.push({ itemId, input, index: i });
+            }
+            catch (err) {
+                errors.push({
+                    index: i,
+                    title: input.title,
+                    error: `ID generation failed: ${err instanceof Error ? err.message : String(err)}`,
+                });
+            }
+        }
+        if (itemsWithIds.length === 0) {
+            return formatToolResult(success({
+                created: 0,
+                items: [],
+                errors,
+            }));
+        }
+        // Build insert rows and WorkItem data blobs
+        const insertRows = [];
+        const workItemMap = new Map();
+        for (const { itemId, input } of itemsWithIds) {
+            const workItem = {
+                id: itemId,
+                type: input.type,
+                title: input.title,
+                summary: input.summary,
+                body: input.body,
+                tags: {
+                    domains: input.domains ?? [],
+                    level: input.level,
+                },
+                ownership: {
+                    primary: null,
+                    additional: [],
+                },
+                relationships: {
+                    parents: input.parent_id ? [input.parent_id] : [],
+                    children: [],
+                    related: [],
+                },
+                links: [],
+                metadata: {
+                    created_at: now,
+                    created_by: userId,
+                    updated_at: now,
+                    updated_by: userId,
+                },
+            };
+            workItemMap.set(itemId, workItem);
+            insertRows.push({
+                id: itemId,
+                project_id: params.project_id,
+                type: input.type,
+                title: input.title,
+                data: workItem,
+                created_by: userId,
+                updated_by: userId,
+            });
+        }
+        // Batch insert all items
+        const { error: insertErr } = await client
+            .from("items")
+            .insert(insertRows);
+        if (insertErr) {
+            // If batch insert fails, fall back to individual inserts
+            for (const { itemId, input, index } of itemsWithIds) {
+                const row = insertRows.find((r) => r.id === itemId);
+                if (!row)
+                    continue;
+                const { error: singleErr } = await client
+                    .from("items")
+                    .insert(row);
+                if (singleErr) {
+                    errors.push({
+                        index,
+                        title: input.title,
+                        error: singleErr.message,
+                    });
+                }
+                else {
+                    created.push({ id: itemId, title: input.title, type: input.type });
+                }
+            }
+        }
+        else {
+            // Batch succeeded — all items created
+            for (const { itemId, input } of itemsWithIds) {
+                created.push({ id: itemId, title: input.title, type: input.type });
+            }
+        }
+        // Create relationships for items with parent_id (fire-and-forget)
+        const relRows = itemsWithIds
+            .filter(({ input }) => input.parent_id)
+            .filter(({ itemId }) => created.some((c) => c.id === itemId))
+            .map(({ itemId, input }) => ({
+            from_id: itemId,
+            to_id: input.parent_id,
+            type: "parent",
+            project_id: params.project_id,
+        }));
+        if (relRows.length > 0) {
+            await client
+                .from("item_relationships")
+                .insert(relRows)
+                .then(({ error }) => {
+                if (error) {
+                    process.stderr.write(`[atoms-mcp] Warning: bulk relationship sync failed: ${error.message}\n`);
+                }
+            });
+        }
+        // Audit: log one change_history entry per created item (fire-and-forget)
+        const historyRows = created.map((item) => ({
+            item_id: item.id,
+            project_id: params.project_id,
+            changed_by: userId,
+            event_type: "created",
+            old_data: null,
+            new_data: workItemMap.get(item.id) ?? null,
+            actor: "mcp_claude",
+            session_id: sessionId,
+        }));
+        if (historyRows.length > 0) {
+            await client
+                .from("change_history")
+                .insert(historyRows)
+                .then(({ error }) => {
+                if (error) {
+                    process.stderr.write(`[atoms-mcp] Warning: bulk change_history log failed: ${error.message}\n`);
+                }
+            });
+        }
+        return formatToolResult(success({
+            created: created.length,
+            items: created,
+            errors: errors.length > 0 ? errors : [],
+            project_id: params.project_id,
+        }));
+    }
+    catch (err) {
+        if (err instanceof Error && err.message.includes("Not authenticated")) {
+            return formatErrorResult(authError());
+        }
+        return formatErrorResult(dbError(err instanceof Error ? err.message : String(err)));
+    }
+}
+//# sourceMappingURL=bulk-import.js.map

package/dist/tools/bulk-import.js.map

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package/dist/tools/project-summary.d.ts

@@ -0,0 +1,64 @@
+/**
+ * atoms_project_summary — One-call compliance/health dashboard for a project.
+ *
+ * Returns item counts by type, test status breakdown, coverage stats
+ * (overall + per domain), and recent change activity.
+ */
+interface DomainCoverage {
+    domain: string;
+    covered: number;
+    total: number;
+    percent: number;
+}
+interface ProjectSummaryData {
+    project_id: string;
+    project_name: string;
+    counts: {
+        requirements: number;
+        test_cases: number;
+        notes: number;
+    };
+    test_status: {
+        passed: number;
+        failed: number;
+        blocked: number;
+        not_run: number;
+    };
+    coverage: {
+        covered: number;
+        uncovered: number;
+        total: number;
+        percent: number;
+    };
+    coverage_by_domain: DomainCoverage[];
+    recent_changes: number;
+    last_updated: string;
+}
+export declare function projectSummaryHandler(params: {
+    project_id: string;
+}): Promise<{
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    structuredContent: {
+        data: any[];
+        meta: {
+            truncated: boolean;
+            truncation_message: string;
+            total_count?: number | undefined;
+            limit?: number | undefined;
+            offset?: number | undefined;
+            has_more?: boolean | undefined;
+        };
+        status: "success";
+    };
+} | {
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    structuredContent: import("../types/responses.js").ToolError | import("../types/responses.js").ToolSuccess<ProjectSummaryData>;
+}>;
+export {};
+//# sourceMappingURL=project-summary.d.ts.map

package/dist/tools/project-summary.d.ts.map

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package/dist/tools/project-summary.js

@@ -0,0 +1,170 @@
+/**
+ * atoms_project_summary — One-call compliance/health dashboard for a project.
+ *
+ * Returns item counts by type, test status breakdown, coverage stats
+ * (overall + per domain), and recent change activity.
+ */
+import { getClient } from "../db/client.js";
+import { formatToolResult, formatErrorResult, success, dbError, authError, notFoundError, } from "./_base.js";
+export async function projectSummaryHandler(params) {
+    try {
+        const client = await getClient();
+        // 1. Verify project exists and get its name
+        const { data: project, error: projErr } = await client
+            .from("projects")
+            .select("id, name")
+            .eq("id", params.project_id)
+            .is("deleted_at", null)
+            .maybeSingle();
+        if (projErr)
+            throw new Error(projErr.message);
+        if (!project) {
+            return formatErrorResult(notFoundError("Project", params.project_id));
+        }
+        // 2. Get all items grouped by type
+        const { data: items, error: itemsErr } = await client
+            .from("items")
+            .select("id, type, data")
+            .eq("project_id", params.project_id)
+            .is("deleted_at", null);
+        if (itemsErr)
+            throw new Error(itemsErr.message);
+        const allItems = items ?? [];
+        const counts = {
+            requirements: 0,
+            test_cases: 0,
+            notes: 0,
+        };
+        const testCaseIds = [];
+        const requirementItems = [];
+        for (const item of allItems) {
+            if (item.type === "requirement") {
+                counts.requirements++;
+                const domains = item.data?.tags?.domains ?? [];
+                requirementItems.push({ id: item.id, domains });
+            }
+            else if (item.type === "test-case") {
+                counts.test_cases++;
+                testCaseIds.push(item.id);
+            }
+            else if (item.type === "note") {
+                counts.notes++;
+            }
+        }
+        // 3. Get latest test result per test case from test_results shadow table
+        const testStatus = {
+            passed: 0,
+            failed: 0,
+            blocked: 0,
+            not_run: 0,
+        };
+        if (testCaseIds.length > 0) {
+            // Fetch all test results for this project, ordered by run_at desc
+            const { data: results, error: resultsErr } = await client
+                .from("test_results")
+                .select("item_id, result, run_at")
+                .eq("project_id", params.project_id)
+                .order("run_at", { ascending: false });
+            if (resultsErr)
+                throw new Error(resultsErr.message);
+            // Deduplicate to latest result per test case
+            const latestByItem = new Map();
+            for (const r of results ?? []) {
+                if (!latestByItem.has(r.item_id)) {
+                    latestByItem.set(r.item_id, r.result);
+                }
+            }
+            // Count statuses — test cases without any result are "not_run"
+            for (const tcId of testCaseIds) {
+                const result = latestByItem.get(tcId);
+                if (!result || result === "not-run") {
+                    testStatus.not_run++;
+                }
+                else if (result === "passed") {
+                    testStatus.passed++;
+                }
+                else if (result === "failed") {
+                    testStatus.failed++;
+                }
+                else if (result === "blocked") {
+                    testStatus.blocked++;
+                }
+                else {
+                    testStatus.not_run++;
+                }
+            }
+        }
+        // 4. Coverage: requirements with at least one verified_by relationship
+        const { data: verifiedRels, error: relErr } = await client
+            .from("item_relationships")
+            .select("from_id")
+            .eq("project_id", params.project_id)
+            .eq("type", "verified_by");
+        if (relErr)
+            throw new Error(relErr.message);
+        const coveredIds = new Set((verifiedRels ?? []).map((r) => r.from_id));
+        const coveredCount = requirementItems.filter((r) => coveredIds.has(r.id)).length;
+        const totalReqs = requirementItems.length;
+        const coverage = {
+            covered: coveredCount,
+            uncovered: totalReqs - coveredCount,
+            total: totalReqs,
+            percent: totalReqs > 0
+                ? Math.round((coveredCount / totalReqs) * 1000) / 10
+                : 100,
+        };
+        // 5. Coverage by domain
+        const domainMap = new Map();
+        for (const req of requirementItems) {
+            const domains = req.domains.length > 0 ? req.domains : ["(untagged)"];
+            const isCovered = coveredIds.has(req.id);
+            for (const domain of domains) {
+                if (!domainMap.has(domain)) {
+                    domainMap.set(domain, { covered: 0, total: 0 });
+                }
+                const entry = domainMap.get(domain);
+                entry.total++;
+                if (isCovered)
+                    entry.covered++;
+            }
+        }
+        const coverageByDomain = Array.from(domainMap.entries())
+            .sort((a, b) => a[0].localeCompare(b[0]))
+            .map(([domain, stats]) => ({
+            domain,
+            covered: stats.covered,
+            total: stats.total,
+            percent: stats.total > 0
+                ? Math.round((stats.covered / stats.total) * 1000) / 10
+                : 100,
+        }));
+        // 6. Recent changes (last 7 days)
+        const sevenDaysAgo = new Date();
+        sevenDaysAgo.setDate(sevenDaysAgo.getDate() - 7);
+        const { count: recentChanges, error: histErr } = await client
+            .from("change_history")
+            .select("id", { count: "exact", head: true })
+            .eq("project_id", params.project_id)
+            .gte("changed_at", sevenDaysAgo.toISOString());
+        if (histErr)
+            throw new Error(histErr.message);
+        const data = {
+            project_id: params.project_id,
+            project_name: project.name,
+            counts,
+            test_status: testStatus,
+            coverage,
+            coverage_by_domain: coverageByDomain,
+            recent_changes: recentChanges ?? 0,
+            last_updated: new Date().toISOString(),
+        };
+        return formatToolResult(success(data));
+    }
+    catch (err) {
+        if (err instanceof Error && err.message.includes("Not authenticated")) {
+            return formatErrorResult(authError());
+        }
+        return formatErrorResult(dbError(err instanceof Error ? err.message : String(err)));
+    }
+}
+//# sourceMappingURL=project-summary.js.map

package/dist/tools/project-summary.js.map

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package/dist/tools/trace.d.ts

@@ -0,0 +1,53 @@
+/**
+ * atoms_trace — Graph traversal for traceability queries.
+ *
+ * Answers questions like "which requirements does TC-00003 verify?"
+ * or "what's affected if I change REQ-00001?"
+ */
+interface TraceNode {
+    id: string;
+    title: string;
+    type: string;
+    relationship: string;
+    depth: number;
+}
+export declare function traceHandler(params: {
+    project_id: string;
+    item_id: string;
+    direction: "upstream" | "downstream" | "both";
+    depth: number;
+    relationship_types?: string[];
+}): Promise<{
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    structuredContent: {
+        data: any[];
+        meta: {
+            truncated: boolean;
+            truncation_message: string;
+            total_count?: number | undefined;
+            limit?: number | undefined;
+            offset?: number | undefined;
+            has_more?: boolean | undefined;
+        };
+        status: "success";
+    };
+} | {
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    structuredContent: import("../types/responses.js").ToolError | import("../types/responses.js").ToolSuccess<{
+        truncated?: boolean | undefined;
+        truncation_message?: string | undefined;
+        root: string;
+        direction: "upstream" | "downstream" | "both";
+        depth_limit: number;
+        items: TraceNode[];
+        total_count: number;
+    }>;
+}>;
+export {};
+//# sourceMappingURL=trace.d.ts.map

package/dist/tools/trace.d.ts.map

@@ -0,0 +1 @@
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package/dist/tools/trace.js

@@ -0,0 +1,166 @@
+/**
+ * atoms_trace — Graph traversal for traceability queries.
+ *
+ * Answers questions like "which requirements does TC-00003 verify?"
+ * or "what's affected if I change REQ-00001?"
+ */
+import { getClient } from "../db/client.js";
+import { getItemById } from "../db/queries.js";
+import { formatToolResult, formatErrorResult, success, notFoundError, dbError, authError, } from "./_base.js";
+/** Maximum items returned to prevent huge responses. */
+const MAX_ITEMS = 200;
+/** Relationship types that point "upstream" (toward parents / dependencies). */
+const UPSTREAM_TYPES = ["parent", "verifies"];
+/** Relationship types that point "downstream" (toward dependents). */
+const DOWNSTREAM_TYPES = ["child", "verified_by"];
+/**
+ * Inverse mapping: when traversing an incoming edge we need
+ * to know what the outgoing type means for the other side.
+ */
+const INVERSE_TYPE = {
+    parent: "child",
+    child: "parent",
+    verifies: "verified_by",
+    verified_by: "verifies",
+    related: "related",
+};
+export async function traceHandler(params) {
+    try {
+        const maxDepth = Math.min(Math.max(params.depth ?? 5, 1), 10);
+        const client = await getClient();
+        // Verify root item exists
+        const rootItem = await getItemById(client, params.project_id, params.item_id);
+        if (!rootItem) {
+            return formatErrorResult(notFoundError("Item", params.item_id));
+        }
+        // Fetch all relationships in the project once (same pattern as export-mermaid)
+        const { data: rels, error: relsErr } = await client
+            .from("item_relationships")
+            .select("from_id, to_id, type")
+            .eq("project_id", params.project_id);
+        if (relsErr)
+            throw new Error(relsErr.message);
+        // Fetch all non-deleted items for title/type lookup
+        const { data: items, error: itemsErr } = await client
+            .from("items")
+            .select("id, title, type")
+            .eq("project_id", params.project_id)
+            .is("deleted_at", null);
+        if (itemsErr)
+            throw new Error(itemsErr.message);
+        const itemMap = new Map();
+        for (const item of items ?? []) {
+            itemMap.set(item.id, { title: item.title, type: item.type });
+        }
+        // Build adjacency lists based on direction
+        // For each item, we store { neighbor, relType, direction }
+        const adjacency = new Map();
+        const addEdge = (from, to, relType) => {
+            if (!adjacency.has(from))
+                adjacency.set(from, []);
+            adjacency.get(from).push({ neighbor: to, relType });
+        };
+        const allowedTypes = params.relationship_types
+            ? new Set(params.relationship_types)
+            : null;
+        for (const rel of rels ?? []) {
+            const relType = rel.type;
+            // Upstream: follow edges where the item is the source and the rel points upstream
+            // i.e., from_id -> to_id with type "parent" or "verifies"
+            if (params.direction === "upstream" || params.direction === "both") {
+                if (UPSTREAM_TYPES.includes(relType)) {
+                    if (!allowedTypes || allowedTypes.has(relType)) {
+                        addEdge(rel.from_id, rel.to_id, relType);
+                    }
+                }
+                // Also follow inverse: if from_id has a "child" pointing to to_id,
+                // then to_id is upstream of from_id — but we model it as:
+                // from_id's downstream is to_id via "child". For upstream from to_id,
+                // we'd follow to_id -> from_id via inverse of "child" = "parent".
+                if (DOWNSTREAM_TYPES.includes(relType)) {
+                    const inverseType = INVERSE_TYPE[relType] ?? relType;
+                    if (!allowedTypes || allowedTypes.has(inverseType)) {
+                        addEdge(rel.to_id, rel.from_id, inverseType);
+                    }
+                }
+            }
+            if (params.direction === "downstream" || params.direction === "both") {
+                if (DOWNSTREAM_TYPES.includes(relType)) {
+                    if (!allowedTypes || allowedTypes.has(relType)) {
+                        addEdge(rel.from_id, rel.to_id, relType);
+                    }
+                }
+                // Inverse: upstream type from the other side means downstream for us
+                if (UPSTREAM_TYPES.includes(relType)) {
+                    const inverseType = INVERSE_TYPE[relType] ?? relType;
+                    if (!allowedTypes || allowedTypes.has(inverseType)) {
+                        addEdge(rel.to_id, rel.from_id, inverseType);
+                    }
+                }
+            }
+            // "related" is bidirectional — add both directions if allowed
+            if (relType === "related") {
+                if (!allowedTypes || allowedTypes.has("related")) {
+                    addEdge(rel.from_id, rel.to_id, "related");
+                    addEdge(rel.to_id, rel.from_id, "related");
+                }
+            }
+        }
+        // BFS traversal from root
+        const visited = new Set();
+        visited.add(params.item_id);
+        const result = [];
+        const queue = [];
+        // Seed queue with direct neighbors of the root
+        const rootNeighbors = adjacency.get(params.item_id) ?? [];
+        for (const edge of rootNeighbors) {
+            queue.push({ id: edge.neighbor, depth: 1, relType: edge.relType });
+        }
+        while (queue.length > 0 && result.length < MAX_ITEMS) {
+            const { id, depth, relType } = queue.shift();
+            if (visited.has(id) || depth > maxDepth)
+                continue;
+            visited.add(id);
+            const info = itemMap.get(id);
+            if (!info)
+                continue; // skip deleted items
+            result.push({
+                id,
+                title: info.title,
+                type: info.type,
+                relationship: relType,
+                depth,
+            });
+            // Enqueue neighbors at next depth
+            if (depth < maxDepth) {
+                const neighbors = adjacency.get(id) ?? [];
+                for (const edge of neighbors) {
+                    if (!visited.has(edge.neighbor)) {
+                        queue.push({
+                            id: edge.neighbor,
+                            depth: depth + 1,
+                            relType: edge.relType,
+                        });
+                    }
+                }
+            }
+        }
+        return formatToolResult(success({
+            root: params.item_id,
+            direction: params.direction,
+            depth_limit: maxDepth,
+            items: result,
+            total_count: result.length,
+            ...(result.length >= MAX_ITEMS
+                ? { truncated: true, truncation_message: `Results capped at ${MAX_ITEMS} items. Use a smaller depth or filter by relationship_types.` }
+                : {}),
+        }));
+    }
+    catch (err) {
+        if (err instanceof Error && err.message.includes("Not authenticated")) {
+            return formatErrorResult(authError());
+        }
+        return formatErrorResult(dbError(err instanceof Error ? err.message : String(err)));
+    }
+}
+//# sourceMappingURL=trace.js.map

package/dist/tools/trace.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@atoms-tech/atoms-mcp",
-  "version": "0.1.1",
+  "version": "0.2.1",
   "description": "MCP server for ATOMS.tech — AI agent integration for requirements management",
   "type": "module",
   "main": "dist/index.js",