@egentica/codemap 0.1.5

package/dist/mcp/server.js

@@ -0,0 +1,264 @@
+#!/usr/bin/env node
+"use strict";
+/**
+ * CodeMap MCP Server (ToolRegistry Edition)
+ *
+ * Exposes CodeMap as an MCP server using auto-discovered tools via ToolRegistry.
+ * Compatible with stdio transport (the standard way Claude connects to MCP servers).
+ *
+ * Plugin-agnostic: Loads plugins dynamically from .codemap/config.json
+ *
+ * Usage:
+ *   npx @egentica/codemap-server
+ *
+ * Configuration via environment variables:
+ *   CODEMAP_ROOT - Root directory to scan (default: current directory)
+ */
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.switchProject = switchProject;
+exports.ensureInitialized = ensureInitialized;
+const mcp_js_1 = require("@modelcontextprotocol/sdk/server/mcp.js");
+const stdio_js_1 = require("@modelcontextprotocol/sdk/server/stdio.js");
+const CodeMap_js_1 = require("../core/CodeMap.js");
+const NodeFsProvider_js_1 = require("../storage/NodeFsProvider.js");
+const ToolRegistry_js_1 = require("./registry/ToolRegistry.js");
+const ParserRegistry_js_1 = require("../core/ParserRegistry.js");
+const help_js_1 = require("./operations/help.js");
+const version_js_1 = require("../utils/version.js");
+// @ts-ignore
+const path_1 = __importDefault(require("path"));
+// @ts-ignore
+const fs_1 = __importDefault(require("fs"));
+// ── Server State ─────────────────────────────────────────────────────────────
+let codemap = null;
+let rootPath = null;
+const provider = new NodeFsProvider_js_1.NodeFsProvider();
+// Config lockdown state
+let configWatcher = null;
+let configSnapshot = null;
+let isRestoringConfig = false; // Prevent infinite loop during restore
+const DEFAULT_CONFIG = {
+    scan: {
+        ignorePatterns: [
+            'node_modules/**',
+            '.git/**',
+            'dist/**',
+            'build/**',
+            '.codemap/**'
+        ],
+        maxFileSize: 1024 * 1024, // 1MB
+        maxDepth: null,
+        followSymlinks: false
+    },
+    plugins: {
+        autoload: true,
+        paths: [],
+        enabled: [],
+        disabled: []
+    }
+};
+function loadConfig(projectRoot) {
+    const configPath = path_1.default.join(projectRoot, '.codemap', 'config.json');
+    if (fs_1.default.existsSync(configPath)) {
+        try {
+            const content = fs_1.default.readFileSync(configPath, 'utf-8');
+            const config = JSON.parse(content);
+            return { ...DEFAULT_CONFIG, ...config };
+        }
+        catch (error) {
+            console.error('[CodeMap] Failed to load config:', error);
+            return DEFAULT_CONFIG;
+        }
+    }
+    return DEFAULT_CONFIG;
+}
+// ── CodeMap Initialization ───────────────────────────────────────────────────
+/**
+ * Initialize CodeMap for a project directory.
+ * This is called lazily by orient/session_start tools, not on server startup.
+ *
+ * @param projectRoot - Project root directory
+ * @param performScan - Whether to perform initial scan (default: true)
+ * @param ctx - Shared operation context to update
+ */
+async function initializeCodeMap(projectRoot, performScan = true, ctx) {
+    // Shutdown previous config lockdown if switching projects
+    if (rootPath && rootPath !== projectRoot) {
+        console.error('[CodeMap] Switching project from:', rootPath, 'to:', projectRoot);
+        shutdownConfigLockdown();
+    }
+    rootPath = projectRoot;
+    const config = loadConfig(projectRoot);
+    console.error('[CodeMap] Initializing for:', projectRoot);
+    codemap = new CodeMap_js_1.CodeMap({
+        rootPath: projectRoot,
+        provider,
+        ignorePatterns: config.scan?.ignorePatterns,
+        bypassHardcodedIgnoreList: config.scan?.bypassHardcodedIgnoreList
+    });
+    // Auto-load bundled parsers (TypeScript and Vue)
+    console.error('[CodeMap] Loading bundled parsers...');
+    const parserRegistry = new ParserRegistry_js_1.ParserRegistry();
+    await parserRegistry.autoloadParsers(codemap, config);
+    // Register with CodeMap for access by tools
+    codemap.setParserRegistry(parserRegistry);
+    const loaded = parserRegistry.getLoadedParsers();
+    console.error('[CodeMap] Loaded parsers:');
+    for (const parser of loaded) {
+        console.error(`  ✓ ${parser.name} v${parser.version}: ${parser.extensions.join(', ')}`);
+    }
+    // Register core help topics
+    console.error('[CodeMap] Registering core help topics...');
+    await (0, help_js_1.registerCoreHelpTopics)(codemap.helpRegistry);
+    console.error('[CodeMap] ✓ Core help topics registered');
+    // Load groups from disk
+    console.error('[CodeMap] Loading groups...');
+    await codemap.groupStore.load();
+    const groupStats = codemap.groupStore.getStats();
+    console.error(`[CodeMap] ✓ Loaded ${groupStats.totalGroups} group(s) with ${groupStats.totalMembers} member(s)`);
+    // Load labels from disk
+    console.error('[CodeMap] Loading labels...');
+    await codemap.labelStore.load();
+    const labelStats = await codemap.labelStore.list();
+    const labelCount = 'labels' in labelStats ? labelStats.labels.length : 0;
+    console.error(`[CodeMap] ✓ Loaded ${labelCount} label(s)`);
+    // Perform initial scan if requested
+    if (performScan) {
+        await codemap.scan();
+        const stats = codemap.getStats();
+        console.error(`[CodeMap] Scan complete: ${stats.files} files, ${stats.symbols} symbols`);
+    }
+    // Setup config lockdown
+    setupConfigLockdown(projectRoot);
+    // Update shared context if provided
+    if (ctx) {
+        ctx.codemap = codemap;
+        ctx.rootPath = rootPath;
+    }
+}
+/**
+ * Switch to a different project directory.
+ * Reinitializes CodeMap with the new root path.
+ *
+ * @param newRootPath - New project root directory
+ * @param performScan - Whether to perform initial scan (default: true)
+ * @returns Updated context with new CodeMap instance
+ */
+async function switchProject(newRootPath, performScan = true) {
+    await initializeCodeMap(newRootPath, performScan);
+    if (!codemap || !rootPath) {
+        throw new Error('CodeMap reinitialization failed');
+    }
+    return {
+        codemap,
+        rootPath
+    };
+}
+/**
+ * Get or initialize CodeMap for a project.
+ * Called by orient/session_start tools to ensure CodeMap is initialized.
+ *
+ * @param projectRoot - Project root directory
+ * @param performScan - Whether to perform initial scan (default: true)
+ * @param ctx - Shared operation context to update
+ */
+async function ensureInitialized(projectRoot, performScan, ctx) {
+    // If already initialized for this project, do nothing
+    if (codemap && rootPath === projectRoot) {
+        console.error('[CodeMap] Already initialized for:', projectRoot);
+        return;
+    }
+    // Initialize for the new project
+    await initializeCodeMap(projectRoot, performScan, ctx);
+}
+// ── Config Lockdown (Prevent Tampering) ─────────────────────────────────────
+function setupConfigLockdown(projectRoot) {
+    const configPath = path_1.default.join(projectRoot, '.codemap', 'config.json');
+    if (!fs_1.default.existsSync(configPath)) {
+        return; // No config file to protect
+    }
+    try {
+        // Take snapshot of current config
+        configSnapshot = fs_1.default.readFileSync(configPath, 'utf-8');
+        // Watch for changes
+        configWatcher = fs_1.default.watch(configPath, (eventType) => {
+            if (eventType === 'change' && !isRestoringConfig) {
+                const current = fs_1.default.readFileSync(configPath, 'utf-8');
+                if (current !== configSnapshot) {
+                    console.error('[CodeMap] ⚠️  Config file modified - restoring original');
+                    isRestoringConfig = true;
+                    fs_1.default.writeFileSync(configPath, configSnapshot);
+                    isRestoringConfig = false;
+                }
+            }
+        });
+        console.error('[CodeMap] Config lockdown enabled');
+    }
+    catch (error) {
+        console.error('[CodeMap] Failed to setup config lockdown:', error);
+    }
+}
+function shutdownConfigLockdown() {
+    if (configWatcher) {
+        configWatcher.close();
+        configWatcher = null;
+        console.error('[CodeMap] Config lockdown disabled');
+    }
+}
+// ── Server Setup ─────────────────────────────────────────────────────────────
+async function main() {
+    console.error('[CodeMap] Starting MCP server (lazy initialization mode)');
+    console.error('[CodeMap] CodeMap will initialize when orient or session_start is called');
+    // Create operation context (initially null - will be populated by orient/session_start)
+    // TypeScript sees non-null types, but runtime starts with null until initialized
+    const ctx = {
+        codemap: null,
+        rootPath: null
+    };
+    // Create MCP server
+    const server = new mcp_js_1.McpServer({
+        name: '@egentica/codemap',
+        version: (0, version_js_1.getVersion)()
+    }, {
+        capabilities: {
+            tools: {}
+        }
+    });
+    // Create tool registry (pass undefined for eventBus since it's private)
+    const registry = new ToolRegistry_js_1.ToolRegistry();
+    // Resolve tools directory relative to this file
+    const toolsDir = path_1.default.join(__dirname, 'tools');
+    console.error('[CodeMap] Loading tools from:', toolsDir);
+    // Auto-discover and load all .tool.js files
+    await registry.loadTools(toolsDir);
+    // Register all tools with the MCP server
+    registry.registerAll(server, ctx);
+    // Connect via stdio transport
+    const transport = new stdio_js_1.StdioServerTransport();
+    await server.connect(transport);
+    console.error('[CodeMap MCP] Server running on stdio');
+    console.error('[CodeMap MCP] Loaded', registry.count, 'tools');
+    console.error('[CodeMap MCP] Waiting for orient or session_start to initialize project...');
+}
+// ── Entry Point ──────────────────────────────────────────────────────────────
+// Cleanup on process exit
+process.on('SIGINT', () => {
+    shutdownConfigLockdown();
+    process.exit(0);
+});
+process.on('SIGTERM', () => {
+    shutdownConfigLockdown();
+    process.exit(0);
+});
+process.on('exit', () => {
+    shutdownConfigLockdown();
+});
+main().catch((error) => {
+    console.error('[CodeMap MCP] Fatal error:', error);
+    shutdownConfigLockdown();
+    process.exit(1);
+});
+//# sourceMappingURL=server.js.map

package/dist/mcp/server.js.map

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package/dist/mcp/tools/annotations/add.tool.d.ts

@@ -0,0 +1,10 @@
+import { z } from 'zod';
+import type { ToolDefinition, ToolHandler } from '../../registry/types.js';
+export declare const inputSchema: z.ZodObject<{
+    path: z.ZodString;
+    key: z.ZodString;
+    value: z.ZodString;
+}, z.core.$strip>;
+export declare const metadata: ToolDefinition;
+export declare const handler: ToolHandler<typeof inputSchema>;
+//# sourceMappingURL=add.tool.d.ts.map

package/dist/mcp/tools/annotations/add.tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"add.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp/tools/annotations/add.tool.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AACxB,OAAO,KAAK,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAI3E,eAAO,MAAM,WAAW;;;;iBAItB,CAAC;AAGH,eAAO,MAAM,QAAQ,EAAE,cAKtB,CAAC;AAGF,eAAO,MAAM,OAAO,EAAE,WAAW,CAAC,OAAO,WAAW,CA0EnD,CAAC"}

package/dist/mcp/tools/annotations/add.tool.js

@@ -0,0 +1,88 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.handler = exports.metadata = exports.inputSchema = void 0;
+// tools/annotations/add.tool.ts
+const zod_1 = require("zod");
+const schemas_js_1 = require("../../registry/schemas.js");
+// ── Input Schema ─────────────────────────────────────────────────────────────
+exports.inputSchema = zod_1.z.object({
+    path: schemas_js_1.pathSchema,
+    key: schemas_js_1.annotationKeySchema,
+    value: schemas_js_1.annotationValueSchema
+});
+// ── Metadata ─────────────────────────────────────────────────────────────────
+exports.metadata = {
+    name: 'codemap_add_annotation',
+    description: 'Add a @codemap annotation to a file.',
+    category: 'annotations',
+    tags: ['annotations', 'write']
+};
+// ── Handler ──────────────────────────────────────────────────────────────────
+const handler = async (args, ctx) => {
+    try {
+        const { path: filePath, key, value } = args;
+        // Use resolver to get absolute path
+        const resolved = await ctx.codemap.resolver.resolve(filePath);
+        // Check config for storage mode (default: false = external storage)
+        const writeToSource = ctx.codemap.config.annotations?.writeAnnotationsToSource ?? false;
+        if (writeToSource) {
+            // Mode: Write to source file
+            // Read current file content
+            const content = await ctx.codemap.fs.read(resolved.filePath);
+            // Find parser for this file
+            const parser = ctx.codemap.getParserForFile(resolved.filePath);
+            if (!parser || !parser.addAnnotation) {
+                throw new Error(`No parser with annotation support found for ${resolved.filePath}`);
+            }
+            // Add annotation using parser
+            const updatedContent = parser.addAnnotation(content, key, value);
+            // Write back
+            await ctx.codemap.fs.write(resolved.filePath, updatedContent);
+            // Track in session log
+            await ctx.codemap.sessionLog.track('annotation:add:source', resolved.relativePath, { key, value });
+        }
+        else {
+            // Mode: External storage
+            // Format annotation for AnnotationStore (all meta annotations stored as "note" type)
+            // Include key in text for retrieval: "KEY: value"
+            const annotationStr = `@codemap.note [info] ${key}: ${value}`;
+            // Add to annotation store
+            const result = await ctx.codemap.annotationStore.attach(resolved.relativePath, [annotationStr]);
+            if (!result.ok) {
+                throw new Error(result.error || 'Failed to attach annotation');
+            }
+            // Track in session log
+            await ctx.codemap.sessionLog.track('annotation:add:meta', resolved.relativePath, { key, value });
+        }
+        return {
+            content: [{
+                    type: 'text',
+                    text: JSON.stringify({
+                        success: true,
+                        path: resolved.relativePath,
+                        key,
+                        value,
+                        action: 'added',
+                        storage: writeToSource ? 'source' : 'meta'
+                    }, null, 2)
+                }]
+        };
+    }
+    catch (err) {
+        return {
+            content: [{
+                    type: 'text',
+                    text: JSON.stringify({
+                        success: false,
+                        error: {
+                            code: 'ADD_ANNOTATION_ERROR',
+                            message: err instanceof Error ? err.message : String(err)
+                        }
+                    }, null, 2)
+                }],
+            isError: true
+        };
+    }
+};
+exports.handler = handler;
+//# sourceMappingURL=add.tool.js.map

package/dist/mcp/tools/annotations/add.tool.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"add.tool.js","sourceRoot":"","sources":["../../../../src/mcp/tools/annotations/add.tool.ts"],"names":[],"mappings":";;;AAAA,gCAAgC;AAChC,6BAAwB;AAExB,0DAAmG;AAEnG,gFAAgF;AACnE,QAAA,WAAW,GAAG,OAAC,CAAC,MAAM,CAAC;IAClC,IAAI,EAAE,uBAAU;IAChB,GAAG,EAAE,gCAAmB;IACxB,KAAK,EAAE,kCAAqB;CAC7B,CAAC,CAAC;AAEH,gFAAgF;AACnE,QAAA,QAAQ,GAAmB;IACtC,IAAI,EAAE,wBAAwB;IAC9B,WAAW,EAAE,sCAAsC;IACnD,QAAQ,EAAE,aAAa;IACvB,IAAI,EAAE,CAAC,aAAa,EAAE,OAAO,CAAC;CAC/B,CAAC;AAEF,gFAAgF;AACzE,MAAM,OAAO,GAAoC,KAAK,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE;IAC1E,IAAI,CAAC;QACH,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAAI,CAAC;QAE5C,oCAAoC;QACpC,MAAM,QAAQ,GAAG,MAAM,GAAG,CAAC,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;QAE9D,oEAAoE;QACpE,MAAM,aAAa,GAAG,GAAG,CAAC,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,wBAAwB,IAAI,KAAK,CAAC;QAExF,IAAI,aAAa,EAAE,CAAC;YAClB,6BAA6B;YAC7B,4BAA4B;YAC5B,MAAM,OAAO,GAAG,MAAM,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;YAE7D,4BAA4B;YAC5B,MAAM,MAAM,GAAG,GAAG,CAAC,OAAO,CAAC,gBAAgB,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;YAC/D,IAAI,CAAC,MAAM,IAAI,CAAC,MAAM,CAAC,aAAa,EAAE,CAAC;gBACrC,MAAM,IAAI,KAAK,CAAC,+CAA+C,QAAQ,CAAC,QAAQ,EAAE,CAAC,CAAC;YACtF,CAAC;YAED,8BAA8B;YAC9B,MAAM,cAAc,GAAG,MAAM,CAAC,aAAa,CAAC,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,CAAC;YAEjE,aAAa;YACb,MAAM,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,EAAE,cAAc,CAAC,CAAC;YAE9D,uBAAuB;YACvB,MAAM,GAAG,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,uBAAuB,EAAE,QAAQ,CAAC,YAAY,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,CAAC;QACrG,CAAC;aAAM,CAAC;YACN,yBAAyB;YACzB,qFAAqF;YACrF,kDAAkD;YAClD,MAAM,aAAa,GAAG,wBAAwB,GAAG,KAAK,KAAK,EAAE,CAAC;YAE9D,0BAA0B;YAC1B,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,QAAQ,CAAC,YAAY,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC;YAEhG,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,KAAK,IAAI,6BAA6B,CAAC,CAAC;YACjE,CAAC;YAED,uBAAuB;YACvB,MAAM,GAAG,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,qBAAqB,EAAE,QAAQ,CAAC,YAAY,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,CAAC;QACnG,CAAC;QAED,OAAO;YACL,OAAO,EAAE,CAAC;oBACR,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;wBACnB,OAAO,EAAE,IAAI;wBACb,IAAI,EAAE,QAAQ,CAAC,YAAY;wBAC3B,GAAG;wBACH,KAAK;wBACL,MAAM,EAAE,OAAO;wBACf,OAAO,EAAE,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM;qBAC3C,EAAE,IAAI,EAAE,CAAC,CAAC;iBACZ,CAAC;SACH,CAAC;IACJ,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,OAAO;YACL,OAAO,EAAE,CAAC;oBACR,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;wBACnB,OAAO,EAAE,KAAK;wBACd,KAAK,EAAE;4BACL,IAAI,EAAE,sBAAsB;4BAC5B,OAAO,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;yBAC1D;qBACF,EAAE,IAAI,EAAE,CAAC,CAAC;iBACZ,CAAC;YACF,OAAO,EAAE,IAAI;SACd,CAAC;IACJ,CAAC;AACH,CAAC,CAAC;AA1EW,QAAA,OAAO,WA0ElB"}

package/dist/mcp/tools/annotations/edit.tool.d.ts

@@ -0,0 +1,10 @@
+import { z } from 'zod';
+import type { ToolDefinition, ToolHandler } from '../../registry/types.js';
+export declare const inputSchema: z.ZodObject<{
+    path: z.ZodString;
+    key: z.ZodString;
+    value: z.ZodString;
+}, z.core.$strip>;
+export declare const metadata: ToolDefinition;
+export declare const handler: ToolHandler<typeof inputSchema>;
+//# sourceMappingURL=edit.tool.d.ts.map

package/dist/mcp/tools/annotations/edit.tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"edit.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp/tools/annotations/edit.tool.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AACxB,OAAO,KAAK,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAI3E,eAAO,MAAM,WAAW;;;;iBAItB,CAAC;AAGH,eAAO,MAAM,QAAQ,EAAE,cAKtB,CAAC;AAGF,eAAO,MAAM,OAAO,EAAE,WAAW,CAAC,OAAO,WAAW,CAiFnD,CAAC"}

package/dist/mcp/tools/annotations/edit.tool.js

@@ -0,0 +1,92 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.handler = exports.metadata = exports.inputSchema = void 0;
+// tools/annotations/edit.tool.ts
+const zod_1 = require("zod");
+const schemas_js_1 = require("../../registry/schemas.js");
+// ── Input Schema ─────────────────────────────────────────────────────────────
+exports.inputSchema = zod_1.z.object({
+    path: schemas_js_1.pathSchema,
+    key: schemas_js_1.annotationKeySchema,
+    value: schemas_js_1.annotationValueSchema
+});
+// ── Metadata ─────────────────────────────────────────────────────────────────
+exports.metadata = {
+    name: 'codemap_edit_annotation',
+    description: 'Edit an existing @codemap annotation in a file.',
+    category: 'annotations',
+    tags: ['annotations', 'write', 'edit']
+};
+// ── Handler ──────────────────────────────────────────────────────────────────
+const handler = async (args, ctx) => {
+    try {
+        const { path: filePath, key, value } = args;
+        // Use resolver to get absolute path
+        const resolved = await ctx.codemap.resolver.resolve(filePath);
+        // Check config for storage mode (default: false = external storage)
+        const writeToSource = ctx.codemap.config.annotations?.writeAnnotationsToSource ?? false;
+        if (writeToSource) {
+            // Mode: Write to source file
+            // Read current file content
+            const content = await ctx.codemap.fs.read(resolved.filePath);
+            // Find parser for this file
+            const parser = ctx.codemap.getParserForFile(resolved.filePath);
+            if (!parser || !parser.editAnnotation) {
+                throw new Error(`No parser with annotation support found for ${resolved.filePath}`);
+            }
+            // Edit annotation using parser
+            const updatedContent = parser.editAnnotation(content, key, value);
+            // Write back
+            await ctx.codemap.fs.write(resolved.filePath, updatedContent);
+        }
+        else {
+            // Mode: External storage
+            // Get current annotations
+            const annotations = await ctx.codemap.annotationStore.get(resolved.relativePath);
+            // Find the annotation with matching key in meta array
+            // Meta annotations are stored as "note" type with text "KEY: value"
+            const metaIndex = annotations.meta.findIndex(a => a.type === 'note' && a.text.startsWith(`${key}:`));
+            if (metaIndex === -1) {
+                throw new Error(`No annotation with key \"${key}\" found in meta storage for ${resolved.relativePath}`);
+            }
+            // Remove old annotation
+            await ctx.codemap.annotationStore.remove(resolved.relativePath, 'meta', metaIndex);
+            // Add new annotation (all meta annotations stored as "note" type)
+            const annotationStr = `@codemap.note [info] ${key}: ${value}`;
+            const result = await ctx.codemap.annotationStore.attach(resolved.relativePath, [annotationStr]);
+            if (!result.ok) {
+                throw new Error(result.error || 'Failed to attach new annotation');
+            }
+        }
+        return {
+            content: [{
+                    type: 'text',
+                    text: JSON.stringify({
+                        success: true,
+                        path: resolved.relativePath,
+                        key,
+                        value,
+                        action: 'edited',
+                        storage: writeToSource ? 'source' : 'meta'
+                    }, null, 2)
+                }]
+        };
+    }
+    catch (err) {
+        return {
+            content: [{
+                    type: 'text',
+                    text: JSON.stringify({
+                        success: false,
+                        error: {
+                            code: 'EDIT_ANNOTATION_ERROR',
+                            message: err instanceof Error ? err.message : String(err)
+                        }
+                    }, null, 2)
+                }],
+            isError: true
+        };
+    }
+};
+exports.handler = handler;
+//# sourceMappingURL=edit.tool.js.map

package/dist/mcp/tools/annotations/edit.tool.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"edit.tool.js","sourceRoot":"","sources":["../../../../src/mcp/tools/annotations/edit.tool.ts"],"names":[],"mappings":";;;AAAA,iCAAiC;AACjC,6BAAwB;AAExB,0DAAmG;AAEnG,gFAAgF;AACnE,QAAA,WAAW,GAAG,OAAC,CAAC,MAAM,CAAC;IAClC,IAAI,EAAE,uBAAU;IAChB,GAAG,EAAE,gCAAmB;IACxB,KAAK,EAAE,kCAAqB;CAC7B,CAAC,CAAC;AAEH,gFAAgF;AACnE,QAAA,QAAQ,GAAmB;IACtC,IAAI,EAAE,yBAAyB;IAC/B,WAAW,EAAE,iDAAiD;IAC9D,QAAQ,EAAE,aAAa;IACvB,IAAI,EAAE,CAAC,aAAa,EAAE,OAAO,EAAE,MAAM,CAAC;CACvC,CAAC;AAEF,gFAAgF;AACzE,MAAM,OAAO,GAAoC,KAAK,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE;IAC1E,IAAI,CAAC;QACH,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAAI,CAAC;QAE5C,oCAAoC;QACpC,MAAM,QAAQ,GAAG,MAAM,GAAG,CAAC,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;QAE9D,oEAAoE;QACpE,MAAM,aAAa,GAAG,GAAG,CAAC,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,wBAAwB,IAAI,KAAK,CAAC;QAExF,IAAI,aAAa,EAAE,CAAC;YAClB,6BAA6B;YAC7B,4BAA4B;YAC5B,MAAM,OAAO,GAAG,MAAM,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;YAE7D,4BAA4B;YAC5B,MAAM,MAAM,GAAG,GAAG,CAAC,OAAO,CAAC,gBAAgB,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;YAC/D,IAAI,CAAC,MAAM,IAAI,CAAC,MAAM,CAAC,cAAc,EAAE,CAAC;gBACtC,MAAM,IAAI,KAAK,CAAC,+CAA+C,QAAQ,CAAC,QAAQ,EAAE,CAAC,CAAC;YACtF,CAAC;YAED,+BAA+B;YAC/B,MAAM,cAAc,GAAG,MAAM,CAAC,cAAc,CAAC,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,CAAC;YAElE,aAAa;YACb,MAAM,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,EAAE,cAAc,CAAC,CAAC;QAChE,CAAC;aAAM,CAAC;YACN,yBAAyB;YACzB,0BAA0B;YAC1B,MAAM,WAAW,GAAG,MAAM,GAAG,CAAC,OAAO,CAAC,eAAe,CAAC,GAAG,CAAC,QAAQ,CAAC,YAAY,CAAC,CAAC;YAEjF,sDAAsD;YACtD,oEAAoE;YACpE,MAAM,SAAS,GAAG,WAAW,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAC/C,CAAC,CAAC,IAAI,KAAK,MAAM,IAAI,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,GAAG,GAAG,CAAC,CAClD,CAAC;YAEF,IAAI,SAAS,KAAK,CAAC,CAAC,EAAE,CAAC;gBACrB,MAAM,IAAI,KAAK,CAAC,4BAA4B,GAAG,gCAAgC,QAAQ,CAAC,YAAY,EAAE,CAAC,CAAC;YAC1G,CAAC;YAED,wBAAwB;YACxB,MAAM,GAAG,CAAC,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,QAAQ,CAAC,YAAY,EAAE,MAAM,EAAE,SAAS,CAAC,CAAC;YAEnF,kEAAkE;YAClE,MAAM,aAAa,GAAG,wBAAwB,GAAG,KAAK,KAAK,EAAE,CAAC;YAC9D,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,QAAQ,CAAC,YAAY,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC;YAEhG,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,KAAK,IAAI,iCAAiC,CAAC,CAAC;YACrE,CAAC;QACH,CAAC;QAED,OAAO;YACL,OAAO,EAAE,CAAC;oBACR,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;wBACnB,OAAO,EAAE,IAAI;wBACb,IAAI,EAAE,QAAQ,CAAC,YAAY;wBAC3B,GAAG;wBACH,KAAK;wBACL,MAAM,EAAE,QAAQ;wBAChB,OAAO,EAAE,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM;qBAC3C,EAAE,IAAI,EAAE,CAAC,CAAC;iBACZ,CAAC;SACH,CAAC;IACJ,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,OAAO;YACL,OAAO,EAAE,CAAC;oBACR,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;wBACnB,OAAO,EAAE,KAAK;wBACd,KAAK,EAAE;4BACL,IAAI,EAAE,uBAAuB;4BAC7B,OAAO,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;yBAC1D;qBACF,EAAE,IAAI,EAAE,CAAC,CAAC;iBACZ,CAAC;YACF,OAAO,EAAE,IAAI;SACd,CAAC;IACJ,CAAC;AACH,CAAC,CAAC;AAjFW,QAAA,OAAO,WAiFlB"}

package/dist/mcp/tools/annotations/remove.tool.d.ts

@@ -0,0 +1,9 @@
+import { z } from 'zod';
+import type { ToolDefinition, ToolHandler } from '../../registry/types.js';
+export declare const inputSchema: z.ZodObject<{
+    path: z.ZodString;
+    key: z.ZodString;
+}, z.core.$strip>;
+export declare const metadata: ToolDefinition;
+export declare const handler: ToolHandler<typeof inputSchema>;
+//# sourceMappingURL=remove.tool.d.ts.map

package/dist/mcp/tools/annotations/remove.tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"remove.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp/tools/annotations/remove.tool.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AACxB,OAAO,KAAK,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAI3E,eAAO,MAAM,WAAW;;;iBAGtB,CAAC;AAGH,eAAO,MAAM,QAAQ,EAAE,cAKtB,CAAC;AAGF,eAAO,MAAM,OAAO,EAAE,WAAW,CAAC,OAAO,WAAW,CA4EnD,CAAC"}

package/dist/mcp/tools/annotations/remove.tool.js

@@ -0,0 +1,87 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.handler = exports.metadata = exports.inputSchema = void 0;
+// tools/annotations/remove.tool.ts
+const zod_1 = require("zod");
+const schemas_js_1 = require("../../registry/schemas.js");
+// ── Input Schema ─────────────────────────────────────────────────────────────
+exports.inputSchema = zod_1.z.object({
+    path: schemas_js_1.pathSchema,
+    key: schemas_js_1.annotationKeySchema
+});
+// ── Metadata ─────────────────────────────────────────────────────────────────
+exports.metadata = {
+    name: 'codemap_remove_annotation',
+    description: 'Remove a @codemap annotation from a file.',
+    category: 'annotations',
+    tags: ['annotations', 'write', 'delete']
+};
+// ── Handler ──────────────────────────────────────────────────────────────────
+const handler = async (args, ctx) => {
+    try {
+        const { path: filePath, key } = args;
+        // Use resolver to get absolute path
+        const resolved = await ctx.codemap.resolver.resolve(filePath);
+        // Check config for storage mode (default: false = external storage)
+        const writeToSource = ctx.codemap.config.annotations?.writeAnnotationsToSource ?? false;
+        if (writeToSource) {
+            // Mode: Write to source file
+            // Read current file content
+            const content = await ctx.codemap.fs.read(resolved.filePath);
+            // Find parser for this file
+            const parser = ctx.codemap.getParserForFile(resolved.filePath);
+            if (!parser || !parser.removeAnnotation) {
+                throw new Error(`No parser with annotation support found for ${resolved.filePath}`);
+            }
+            // Remove annotation using parser
+            const updatedContent = parser.removeAnnotation(content, key);
+            // Write back
+            await ctx.codemap.fs.write(resolved.filePath, updatedContent);
+        }
+        else {
+            // Mode: External storage
+            // Get current annotations
+            const annotations = await ctx.codemap.annotationStore.get(resolved.relativePath);
+            // Find the annotation with matching key in meta array
+            // Meta annotations are stored as "note" type with text "KEY: value"
+            const metaIndex = annotations.meta.findIndex(a => a.type === 'note' && a.text.startsWith(`${key}:`));
+            if (metaIndex === -1) {
+                throw new Error(`No annotation with key \"${key}\" found in meta storage for ${resolved.relativePath}`);
+            }
+            // Remove annotation
+            const removed = await ctx.codemap.annotationStore.remove(resolved.relativePath, 'meta', metaIndex);
+            if (!removed) {
+                throw new Error('Failed to remove annotation from store');
+            }
+        }
+        return {
+            content: [{
+                    type: 'text',
+                    text: JSON.stringify({
+                        success: true,
+                        path: resolved.relativePath,
+                        key,
+                        action: 'removed',
+                        storage: writeToSource ? 'source' : 'meta'
+                    }, null, 2)
+                }]
+        };
+    }
+    catch (err) {
+        return {
+            content: [{
+                    type: 'text',
+                    text: JSON.stringify({
+                        success: false,
+                        error: {
+                            code: 'REMOVE_ANNOTATION_ERROR',
+                            message: err instanceof Error ? err.message : String(err)
+                        }
+                    }, null, 2)
+                }],
+            isError: true
+        };
+    }
+};
+exports.handler = handler;
+//# sourceMappingURL=remove.tool.js.map

package/dist/mcp/tools/annotations/remove.tool.js.map

@@ -0,0 +1 @@
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package/dist/mcp/tools/annotations/search-annotations.tool.d.ts

@@ -0,0 +1,11 @@
+import { z } from 'zod';
+import type { ToolDefinition, ToolHandler } from '../../registry/types.js';
+export declare const inputSchema: z.ZodObject<{
+    query: z.ZodString;
+    type: z.ZodOptional<z.ZodString>;
+    severity: z.ZodOptional<z.ZodString>;
+    maxResults: z.ZodOptional<z.ZodNumber>;
+}, z.core.$strip>;
+export declare const metadata: ToolDefinition;
+export declare const handler: ToolHandler<typeof inputSchema>;
+//# sourceMappingURL=search-annotations.tool.d.ts.map

package/dist/mcp/tools/annotations/search-annotations.tool.d.ts.map

@@ -0,0 +1 @@
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