@colbymchenry/codegraph 0.7.9 → 0.8.0

package/dist/installer/targets/claude.js

@@ -1,17 +1,21 @@
 "use strict";
 /**
- * Claude Code target — the historical default. Writes:
+ * Claude Code target. Writes:
  *
- *   - MCP server entry to `~/.claude.json` (global) or
- *     `./.claude.json` (local).
+ *   - MCP server entry to `~/.claude.json` (global = user scope, loads
+ *     in every project) or `./.mcp.json` (local = project scope, the
+ *     file Claude Code actually reads for a single project). See the
+ *     scope table at https://code.claude.com/docs/en/mcp.
  *   - Permissions to `~/.claude/settings.json` (global) or
  *     `./.claude/settings.json` (local), gated on `autoAllow`.
  *   - Instructions to `~/.claude/CLAUDE.md` (global) or
  *     `./.claude/CLAUDE.md` (local).
  *
- * All paths and shapes ported verbatim from the original
- * `config-writer.ts` so existing Claude Code installs upgrade in
- * place — no migration on disk required.
+ * Earlier versions wrote the local MCP entry to `./.claude.json` — a
+ * file Claude Code never reads — so the server silently never loaded
+ * until the user manually renamed it to `.mcp.json` (issue #207). We
+ * now write `./.mcp.json` and migrate any stale `./.claude.json` entry
+ * out of the way on install and uninstall.
  */
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
@@ -62,9 +66,22 @@ function configDir(loc) {
         : path.join(process.cwd(), '.claude');
 }
 function mcpJsonPath(loc) {
+    // global → ~/.claude.json (user scope: visible in every project).
+    // local  → ./.mcp.json (project scope: the ONLY project-level MCP
+    // file Claude Code reads — NOT ./.claude.json, which it ignores).
     return loc === 'global'
         ? path.join(os.homedir(), '.claude.json')
-        : path.join(process.cwd(), '.claude.json');
+        : path.join(process.cwd(), '.mcp.json');
+}
+/**
+ * Where pre-#207 installers wrote the local MCP entry. Claude Code
+ * never reads a project-level `./.claude.json`, so we migrate the
+ * codegraph entry out of it on install and strip it on uninstall.
+ * Only the project-local path is legacy — global `~/.claude.json` is
+ * the correct user-scope location and is left untouched.
+ */
+function legacyLocalMcpPath() {
+    return path.join(process.cwd(), '.claude.json');
 }
 function settingsJsonPath(loc) {
     return path.join(configDir(loc), 'settings.json');
@@ -95,6 +112,14 @@ class ClaudeCodeTarget {
         const files = [];
         // 1. MCP server entry
         files.push(writeMcpEntry(loc));
+        // 1b. Migrate away any stale ./.claude.json left by a pre-#207
+        // local install, so the project isn't left with two competing
+        // (one dead) MCP configs.
+        if (loc === 'local') {
+            const migrated = cleanupLegacyLocalMcp();
+            if (migrated)
+                files.push(migrated);
+        }
         // 2. Permissions (only when autoAllow)
         if (opts.autoAllow) {
             files.push(writePermissionsEntry(loc));
@@ -119,6 +144,13 @@ class ClaudeCodeTarget {
         else {
             files.push({ path: mcpPath, action: 'not-found' });
         }
+        // 1b. Also strip the codegraph entry from a legacy ./.claude.json
+        // so uninstall fully reverses a pre-#207 local install.
+        if (loc === 'local') {
+            const migrated = cleanupLegacyLocalMcp();
+            if (migrated)
+                files.push(migrated);
+        }
         // 2. Permissions
         const settingsPath = settingsJsonPath(loc);
         const settings = (0, shared_1.readJsonFile)(settingsPath);
@@ -174,9 +206,10 @@ function writeMcpEntry(loc) {
         return { path: file, action: 'unchanged' };
     }
     // 'created' here means: the file itself did not exist before this
-    // write. A pre-existing `.claude.json` containing other MCP servers
-    // (no `codegraph` key) is 'updated', not 'created' — we're adding
-    // an entry to a file that was already there. Codex uses a different
+    // write. A pre-existing MCP JSON file (`~/.claude.json` globally,
+    // `./.mcp.json` locally) containing other MCP servers (no
+    // `codegraph` key) is 'updated', not 'created' — we're adding an
+    // entry to a file that was already there. Codex uses a different
     // idiom (empty-content => 'created') because its config.toml is
     // ours alone to manage.
     const action = before ? 'updated' : (fs.existsSync(file) ? 'updated' : 'created');
@@ -186,6 +219,35 @@ function writeMcpEntry(loc) {
     (0, shared_1.writeJsonFile)(file, existing);
     return { path: file, action };
 }
+/**
+ * Strip the codegraph entry from a legacy project-local
+ * `./.claude.json` (written by pre-#207 installers, which Claude Code
+ * never read). Surgical: only our `codegraph` key is removed; sibling
+ * MCP servers and any unrelated keys are preserved, and the file is
+ * deleted only when removal leaves it completely empty. Returns the
+ * file action for reporting, or `null` when there's nothing to migrate.
+ */
+function cleanupLegacyLocalMcp() {
+    const file = legacyLocalMcpPath();
+    if (!fs.existsSync(file))
+        return null;
+    const config = (0, shared_1.readJsonFile)(file);
+    if (!config.mcpServers?.codegraph)
+        return null;
+    delete config.mcpServers.codegraph;
+    if (Object.keys(config.mcpServers).length === 0)
+        delete config.mcpServers;
+    if (Object.keys(config).length === 0) {
+        try {
+            fs.unlinkSync(file);
+        }
+        catch { /* ignore */ }
+    }
+    else {
+        (0, shared_1.writeJsonFile)(file, config);
+    }
+    return { path: file, action: 'removed' };
+}
 function writePermissionsEntry(loc) {
     const file = settingsJsonPath(loc);
     const settings = (0, shared_1.readJsonFile)(file);

package/dist/installer/targets/claude.js.map

@@ -1 +1 @@
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+{"version":3,"file":"claude.js","sourceRoot":"","sources":["../../../src/installer/targets/claude.ts"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;GAiBG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAmLH,sCAsBC;AAyBD,sDAoBC;AAED,wDA0CC;AAhSD,uCAAyB;AACzB,2CAA6B;AAC7B,uCAAyB;AAQzB,qCASkB;AAClB,oEAIkC;AAElC,SAAS,SAAS,CAAC,GAAa;IAC9B,OAAO,GAAG,KAAK,QAAQ;QACrB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,OAAO,EAAE,EAAE,SAAS,CAAC;QACpC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,SAAS,CAAC,CAAC;AAC1C,CAAC;AACD,SAAS,WAAW,CAAC,GAAa;IAChC,kEAAkE;IAClE,kEAAkE;IAClE,kEAAkE;IAClE,OAAO,GAAG,KAAK,QAAQ;QACrB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,OAAO,EAAE,EAAE,cAAc,CAAC;QACzC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,WAAW,CAAC,CAAC;AAC5C,CAAC;AACD;;;;;;GAMG;AACH,SAAS,kBAAkB;IACzB,OAAO,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,cAAc,CAAC,CAAC;AAClD,CAAC;AACD,SAAS,gBAAgB,CAAC,GAAa;IACrC,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,eAAe,CAAC,CAAC;AACpD,CAAC;AACD,SAAS,gBAAgB,CAAC,GAAa;IACrC,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,WAAW,CAAC,CAAC;AAChD,CAAC;AAED,MAAM,gBAAgB;IACX,EAAE,GAAG,QAAiB,CAAC;IACvB,WAAW,GAAG,aAAa,CAAC;IAC5B,OAAO,GAAG,6CAA6C,CAAC;IAEjE,gBAAgB,CAAC,IAAc;QAC7B,OAAO,IAAI,CAAC;IACd,CAAC;IAED,MAAM,CAAC,GAAa;QAClB,MAAM,OAAO,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC;QACjC,MAAM,MAAM,GAAG,IAAA,qBAAY,EAAC,OAAO,CAAC,CAAC;QACrC,MAAM,iBAAiB,GAAG,CAAC,CAAC,MAAM,CAAC,UAAU,EAAE,SAAS,CAAC;QACzD,gEAAgE;QAChE,gEAAgE;QAChE,sCAAsC;QACtC,MAAM,SAAS,GAAG,GAAG,KAAK,QAAQ;YAChC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC;YACzD,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,UAAU,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC;QAC5D,OAAO,EAAE,SAAS,EAAE,iBAAiB,EAAE,UAAU,EAAE,OAAO,EAAE,CAAC;IAC/D,CAAC;IAED,OAAO,CAAC,GAAa,EAAE,IAAoB;QACzC,MAAM,KAAK,GAAyB,EAAE,CAAC;QAEvC,sBAAsB;QACtB,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC;QAE/B,+DAA+D;QAC/D,8DAA8D;QAC9D,0BAA0B;QAC1B,IAAI,GAAG,KAAK,OAAO,EAAE,CAAC;YACpB,MAAM,QAAQ,GAAG,qBAAqB,EAAE,CAAC;YACzC,IAAI,QAAQ;gBAAE,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;QACrC,CAAC;QAED,uCAAuC;QACvC,IAAI,IAAI,CAAC,SAAS,EAAE,CAAC;YACnB,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC;QACzC,CAAC;QAED,4BAA4B;QAC5B,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,GAAG,CAAC,CAAC,CAAC;QAExC,OAAO,EAAE,KAAK,EAAE,CAAC;IACnB,CAAC;IAED,SAAS,CAAC,GAAa;QACrB,MAAM,KAAK,GAAyB,EAAE,CAAC;QAEvC,sBAAsB;QACtB,MAAM,OAAO,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC;QACjC,MAAM,MAAM,GAAG,IAAA,qBAAY,EAAC,OAAO,CAAC,CAAC;QACrC,IAAI,MAAM,CAAC,UAAU,EAAE,SAAS,EAAE,CAAC;YACjC,OAAO,MAAM,CAAC,UAAU,CAAC,SAAS,CAAC;YACnC,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAChD,OAAO,MAAM,CAAC,UAAU,CAAC;YAC3B,CAAC;YACD,IAAA,sBAAa,EAAC,OAAO,EAAE,MAAM,CAAC,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC,CAAC;QACnD,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,WAAW,EAAE,CAAC,CAAC;QACrD,CAAC;QAED,kEAAkE;QAClE,wDAAwD;QACxD,IAAI,GAAG,KAAK,OAAO,EAAE,CAAC;YACpB,MAAM,QAAQ,GAAG,qBAAqB,EAAE,CAAC;YACzC,IAAI,QAAQ;gBAAE,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;QACrC,CAAC;QAED,iBAAiB;QACjB,MAAM,YAAY,GAAG,gBAAgB,CAAC,GAAG,CAAC,CAAC;QAC3C,MAAM,QAAQ,GAAG,IAAA,qBAAY,EAAC,YAAY,CAAC,CAAC;QAC5C,IAAI,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,WAAW,EAAE,KAAK,CAAC,EAAE,CAAC;YAC/C,MAAM,MAAM,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC;YACjD,QAAQ,CAAC,WAAW,CAAC,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,CAC5D,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,kBAAkB,CAAC,CACjD,CAAC;YACF,IAAI,QAAQ,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,KAAK,MAAM,EAAE,CAAC;gBACjD,IAAI,QAAQ,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;oBAC5C,OAAO,QAAQ,CAAC,WAAW,CAAC,KAAK,CAAC;gBACpC,CAAC;gBACD,IAAI,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;oBACnD,OAAO,QAAQ,CAAC,WAAW,CAAC;gBAC9B,CAAC;gBACD,IAAA,sBAAa,EAAC,YAAY,EAAE,QAAQ,CAAC,CAAC;gBACtC,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC,CAAC;YACxD,CAAC;iBAAM,CAAC;gBACN,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,MAAM,EAAE,WAAW,EAAE,CAAC,CAAC;YAC1D,CAAC;QACH,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,MAAM,EAAE,WAAW,EAAE,CAAC,CAAC;QAC1D,CAAC;QAED,kBAAkB;QAClB,MAAM,KAAK,GAAG,gBAAgB,CAAC,GAAG,CAAC,CAAC;QACpC,MAAM,MAAM,GAAG,IAAA,4BAAmB,EAAC,KAAK,EAAE,+CAAuB,EAAE,6CAAqB,CAAC,CAAC;QAC1F,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC,CAAC;QAEpC,OAAO,EAAE,KAAK,EAAE,CAAC;IACnB,CAAC;IAED,WAAW,CAAC,GAAa;QACvB,MAAM,MAAM,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC;QAChC,MAAM,OAAO,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,UAAU,EAAE,EAAE,SAAS,EAAE,IAAA,2BAAkB,GAAE,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;QAC7F,OAAO,YAAY,MAAM,OAAO,OAAO,IAAI,CAAC;IAC9C,CAAC;IAED,aAAa,CAAC,GAAa;QACzB,OAAO,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,gBAAgB,CAAC,GAAG,CAAC,EAAE,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAC;IAC1E,CAAC;CACF;AAED;;;;;;GAMG;AACH,SAAgB,aAAa,CAAC,GAAa;IACzC,MAAM,IAAI,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC;IAC9B,MAAM,QAAQ,GAAG,IAAA,qBAAY,EAAC,IAAI,CAAC,CAAC;IACpC,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAAE,SAAS,CAAC;IAC9C,MAAM,KAAK,GAAG,IAAA,2BAAkB,GAA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package/dist/mcp/index.d.ts

@@ -25,6 +25,9 @@ export declare class MCPServer {
     private cg;
     private toolHandler;
     private projectPath;
+    private initPromise;
+    private clientSupportsRoots;
+    private rootsAttempted;
     constructor(projectPath?: string);
     /**
      * Start the MCP server
@@ -49,8 +52,17 @@ export declare class MCPServer {
      * Called lazily on tool calls that need the default project.
      * Re-walks parent directories each time so it picks up projects
      * initialized after the MCP server started.
+     *
+     * Awaits any in-flight background init (kicked off by handleInitialize) so
+     * we never open the SQLite file twice concurrently.
      */
     private retryInitIfNeeded;
+    /**
+     * Resolve the project root via the MCP `roots/list` request and initialize
+     * from the first root the client reports. Falls back to the process cwd if
+     * the client returns no usable root or doesn't answer in time. See issue #196.
+     */
+    private initFromRoots;
     /**
      * Start file watching on the active CodeGraph instance.
      * Logs sync activity to stderr for diagnostics.

package/dist/mcp/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/mcp/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AA6DH;;;;;GAKG;AACH,qBAAa,SAAS;IACpB,OAAO,CAAC,SAAS,CAAiB;IAClC,OAAO,CAAC,EAAE,CAA0B;IACpC,OAAO,CAAC,WAAW,CAAc;IACjC,OAAO,CAAC,WAAW,CAAgB;IAGnC,OAAO,CAAC,WAAW,CAA8B;IAIjD,OAAO,CAAC,mBAAmB,CAAS;IAGpC,OAAO,CAAC,cAAc,CAAS;gBAEnB,WAAW,CAAC,EAAE,MAAM;IAOhC;;;;;OAKG;IACG,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAe5B;;;;;;;;;OASG;YACW,oBAAoB;IAyBlC;;;;;;;;OAQG;YACW,iBAAiB;IA+C/B;;;;OAIG;YACW,aAAa;IAiB3B;;;OAGG;IACH,OAAO,CAAC,aAAa;IAsCrB;;OAEG;IACH,IAAI,IAAI,IAAI;IAYZ;;OAEG;YACW,aAAa;IA6C3B;;OAEG;YACW,gBAAgB;IA6D9B;;OAEG;YACW,eAAe;IAO7B;;OAEG;YACW,eAAe;CAqC9B;AAGD,OAAO,EAAE,cAAc,EAAE,MAAM,aAAa,CAAC;AAC7C,OAAO,EAAE,KAAK,EAAE,WAAW,EAAE,MAAM,SAAS,CAAC"}

package/dist/mcp/index.js

@@ -52,6 +52,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.ToolHandler = exports.tools = exports.StdioTransport = exports.MCPServer = void 0;
 const path = __importStar(require("path"));
 const index_1 = __importStar(require("../index"));
+const sync_1 = require("../sync");
 const transport_1 = require("./transport");
 const tools_1 = require("./tools");
 const server_instructions_1 = require("./server-instructions");
@@ -85,6 +86,27 @@ const SERVER_INFO = {
  * MCP Protocol Version
  */
 const PROTOCOL_VERSION = '2024-11-05';
+/**
+ * How long to wait for the client's `roots/list` response before giving up
+ * and falling back to the process cwd.
+ */
+const ROOTS_LIST_TIMEOUT_MS = 5000;
+/**
+ * Extract the first usable filesystem path from a `roots/list` result.
+ * Shape per MCP spec: `{ roots: [{ uri: "file:///path", name?: string }] }`.
+ * Returns null if the result is empty or malformed.
+ */
+function firstRootPath(result) {
+    if (!result || typeof result !== 'object')
+        return null;
+    const roots = result.roots;
+    if (!Array.isArray(roots) || roots.length === 0)
+        return null;
+    const first = roots[0];
+    if (typeof first?.uri !== 'string')
+        return null;
+    return fileUriToPath(first.uri);
+}
 /**
  * MCP Server for CodeGraph
  *
@@ -96,6 +118,16 @@ class MCPServer {
     cg = null;
     toolHandler;
     projectPath;
+    // In-flight background init kicked off from handleInitialize. Tracked so the
+    // sync retry path doesn't race against it (double-opening the SQLite file).
+    initPromise = null;
+    // Whether the client advertised the MCP `roots` capability during initialize.
+    // If so, and no explicit project path was given, we ask it for the workspace
+    // root via roots/list rather than guessing from the (often wrong) cwd.
+    clientSupportsRoots = false;
+    // Guards the one-shot deferred resolution (roots/list or cwd) so we don't
+    // re-issue roots/list on every tool call.
+    rootsAttempted = false;
     constructor(projectPath) {
         this.projectPath = projectPath || null;
         this.transport = new transport_1.StdioTransport();
@@ -131,6 +163,8 @@ class MCPServer {
      * are still possible.
      */
     async tryInitializeDefault(projectPath) {
+        // Record where we searched so a later "not initialized" error can name it.
+        this.toolHandler.setDefaultProjectHint(projectPath);
         // Walk up parent directories to find nearest .codegraph/
         const resolvedRoot = (0, index_1.findNearestCodeGraphRoot)(projectPath);
         if (!resolvedRoot) {
@@ -154,15 +188,43 @@ class MCPServer {
      * Called lazily on tool calls that need the default project.
      * Re-walks parent directories each time so it picks up projects
      * initialized after the MCP server started.
+     *
+     * Awaits any in-flight background init (kicked off by handleInitialize) so
+     * we never open the SQLite file twice concurrently.
      */
-    retryInitIfNeeded() {
+    async retryInitIfNeeded() {
+        // Wait for the background init started during handleInitialize, if any.
+        if (this.initPromise) {
+            try {
+                await this.initPromise;
+            }
+            catch { /* errored init falls through to retry */ }
+        }
         // Already initialized successfully
         if (this.toolHandler.hasDefaultCodeGraph())
             return;
-        // No project path to retry with
-        if (!this.projectPath)
-            return;
-        const resolvedRoot = (0, index_1.findNearestCodeGraphRoot)(this.projectPath);
+        // No explicit path was given at initialize. Resolve it now, exactly once:
+        // ask the client via roots/list (if it advertised roots), else use cwd.
+        // Deferring to here lets a roots answer override the wrong cwd, and the
+        // one-shot guard means we never re-issue roots/list per tool call.
+        if (!this.projectPath && !this.rootsAttempted) {
+            this.rootsAttempted = true;
+            this.initPromise = (this.clientSupportsRoots
+                ? this.initFromRoots()
+                : this.tryInitializeDefault(process.cwd())).finally(() => { this.initPromise = null; });
+            try {
+                await this.initPromise;
+            }
+            catch { /* fall through to last-resort below */ }
+            if (this.toolHandler.hasDefaultCodeGraph())
+                return;
+        }
+        // Last resort: re-walk from the best candidate we have. Picks up projects
+        // initialized after the server started, and covers clients that sent no
+        // usable initialize signal at all.
+        const candidate = this.projectPath ?? process.cwd();
+        this.toolHandler.setDefaultProjectHint(candidate);
+        const resolvedRoot = (0, index_1.findNearestCodeGraphRoot)(candidate);
         if (!resolvedRoot)
             return;
         try {
@@ -183,6 +245,29 @@ class MCPServer {
             // Still failing — will retry on next tool call
         }
     }
+    /**
+     * Resolve the project root via the MCP `roots/list` request and initialize
+     * from the first root the client reports. Falls back to the process cwd if
+     * the client returns no usable root or doesn't answer in time. See issue #196.
+     */
+    async initFromRoots() {
+        let target = process.cwd();
+        try {
+            const result = await this.transport.request('roots/list', undefined, ROOTS_LIST_TIMEOUT_MS);
+            const rootPath = firstRootPath(result);
+            if (rootPath) {
+                target = rootPath;
+            }
+            else {
+                process.stderr.write('[CodeGraph MCP] Client returned no workspace roots; falling back to process cwd.\n');
+            }
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            process.stderr.write(`[CodeGraph MCP] roots/list request failed (${msg}); falling back to process cwd.\n`);
+        }
+        await this.tryInitializeDefault(target);
+    }
     /**
      * Start file watching on the active CodeGraph instance.
      * Logs sync activity to stderr for diagnostics.
@@ -190,6 +275,15 @@ class MCPServer {
     startWatching() {
         if (!this.cg)
             return;
+        // When the watcher is intentionally disabled (e.g. WSL2 /mnt drives, or
+        // CODEGRAPH_NO_WATCH=1), say so explicitly and tell the user how to keep
+        // the graph fresh — otherwise the silent staleness is hard to diagnose.
+        const disabledReason = (0, sync_1.watchDisabledReason)(this.projectPath ?? process.cwd());
+        if (disabledReason) {
+            process.stderr.write(`[CodeGraph MCP] File watcher disabled — ${disabledReason}. ` +
+                `The graph will not auto-update; run \`codegraph sync\` (or install the git sync hooks via \`codegraph init\`) to refresh.\n`);
+            return;
+        }
         const started = this.cg.watch({
             onSyncComplete: (result) => {
                 if (result.filesChanged > 0) {
@@ -203,6 +297,10 @@ class MCPServer {
         if (started) {
             process.stderr.write('[CodeGraph MCP] File watcher active — graph will auto-sync on changes\n');
         }
+        else {
+            // start() can also return false when recursive fs.watch isn't supported.
+            process.stderr.write('[CodeGraph MCP] File watcher unavailable on this platform — run `codegraph sync` to refresh the graph after changes.\n');
+        }
     }
     /**
      * Stop the server
@@ -260,24 +358,35 @@ class MCPServer {
      */
     async handleInitialize(request) {
         const params = request.params;
-        // Extract project path from rootUri or workspaceFolders
-        let projectPath = this.projectPath;
+        // Does the client support the MCP `roots` protocol? If so, and we have no
+        // explicit path, we ask it for the workspace root after the handshake
+        // instead of falling back to the (frequently wrong) cwd. See issue #196.
+        this.clientSupportsRoots = !!params?.capabilities?.roots;
+        // Explicit project signal, strongest first: a client-provided rootUri /
+        // workspaceFolders (LSP-style, non-standard but some clients send it), else
+        // the --path the server was launched with. cwd is NOT used here — we defer
+        // it so a roots/list answer can win over it.
+        let explicitPath = null;
         if (params?.rootUri) {
-            projectPath = fileUriToPath(params.rootUri);
+            explicitPath = fileUriToPath(params.rootUri);
         }
         else if (params?.workspaceFolders?.[0]?.uri) {
-            projectPath = fileUriToPath(params.workspaceFolders[0].uri);
+            explicitPath = fileUriToPath(params.workspaceFolders[0].uri);
         }
-        // Fall back to current working directory if no path provided
-        if (!projectPath) {
-            projectPath = process.cwd();
+        else if (this.projectPath) {
+            explicitPath = this.projectPath;
         }
-        // Try to initialize the default project (non-fatal if it fails)
-        await this.tryInitializeDefault(projectPath);
-        // We accept the client's protocol version but respond with our supported version.
-        // The `instructions` field is surfaced by MCP clients in the agent's system
-        // prompt automatically — it's the right place for the universal tool-selection
-        // playbook, ahead of individual tool descriptions.
+        // Respond to the handshake BEFORE doing any heavy initialization. Loading
+        // the SQLite DB and the tree-sitter WASM runtime can take many seconds on
+        // slow filesystems (Docker Desktop VirtioFS on macOS, WSL2). Clients like
+        // Claude Code time out the handshake at ~30s, which manifested as
+        // "MCP tools never appear" — the child was alive and had received the
+        // initialize but was still awaiting initGrammars(). See issue #172.
+        //
+        // We accept the client's protocol version but respond with our supported
+        // version. The `instructions` field is surfaced by MCP clients in the
+        // agent's system prompt automatically — it's the right place for the
+        // universal tool-selection playbook, ahead of individual tool descriptions.
         this.transport.sendResult(request.id, {
             protocolVersion: PROTOCOL_VERSION,
             capabilities: {
@@ -286,12 +395,26 @@ class MCPServer {
             serverInfo: SERVER_INFO,
             instructions: server_instructions_1.SERVER_INSTRUCTIONS,
         });
+        // If we know the project dir, kick off init in the background now. Tool
+        // calls that arrive before it finishes fall through to `retryInitIfNeeded`,
+        // which waits for this promise rather than racing it with a second open.
+        //
+        // If we DON'T know it (no rootUri, no --path), defer: the first tool call
+        // resolves it via roots/list (when the client supports roots) or cwd. This
+        // is the fix for issue #196 — clients that launch the server outside the
+        // project and don't pass a rootUri previously got a misleading "not
+        // initialized" error on every call.
+        if (explicitPath) {
+            this.initPromise = this.tryInitializeDefault(explicitPath).finally(() => {
+                this.initPromise = null;
+            });
+        }
     }
     /**
      * Handle tools/list request
      */
     async handleToolsList(request) {
-        this.retryInitIfNeeded();
+        await this.retryInitIfNeeded();
         this.transport.sendResult(request.id, {
             tools: this.toolHandler.getTools(),
         });
@@ -315,7 +438,7 @@ class MCPServer {
         }
         // If the default project isn't initialized yet, retry in case it was
         // initialized after the MCP server started (e.g. user ran codegraph init)
-        this.retryInitIfNeeded();
+        await this.retryInitIfNeeded();
         const result = await this.toolHandler.execute(toolName, toolArgs);
         this.transport.sendResult(request.id, result);
     }

package/dist/mcp/index.js.map

@@ -1 +1 @@
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package/dist/mcp/server-instructions.d.ts

@@ -15,5 +15,5 @@
  * burn tokens. Reference only tools that exist on `main`; gate any
  * conditional tools behind feature checks if/when they ship.
  */
-export declare const SERVER_INSTRUCTIONS = "# Codegraph \u2014 code intelligence over an indexed knowledge graph\n\nCodegraph is a SQLite knowledge graph of every symbol, edge, and file\nin the workspace. Reads are sub-millisecond; the index lags writes by\nabout a second through the file watcher. Consult it BEFORE writing or\nediting code, not during.\n\n## Tool selection by intent\n\n- **\"What is the symbol named X?\"** \u2192 `codegraph_search`\n- **\"What's the deal with this task / feature / area?\"** \u2192 `codegraph_context` (PRIMARY \u2014 composes search + node + callers + callees in one call)\n- **\"What calls this?\"** \u2192 `codegraph_callers`\n- **\"What does this call?\"** \u2192 `codegraph_callees`\n- **\"What would changing this break?\"** \u2192 `codegraph_impact`\n- **\"Show me this symbol's source / signature / docstring.\"** \u2192 `codegraph_node`\n- **\"Survey an unfamiliar topic / pattern / module.\"** \u2192 `codegraph_explore` (heavier; deep dive)\n- **\"What's in directory X?\"** \u2192 `codegraph_files`\n- **\"Is the index ready / what's its size?\"** \u2192 `codegraph_status`\n\n## Common chains\n\n- **Onboarding**: `codegraph_context` first. If still unclear, `codegraph_explore` for breadth, then `codegraph_node` on specific symbols.\n- **Refactor planning**: `codegraph_search` \u2192 `codegraph_callers` \u2192 `codegraph_impact`. The blast-radius answer comes from impact, not from walking callers manually.\n- **Debugging a regression**: `codegraph_callers` of the suspected symbol; widen with `codegraph_impact` if an unexpected call appears.\n\n## Anti-patterns\n\n- **Don't grep first** when looking up a symbol by name \u2014 `codegraph_search` is faster and returns kind + location + signature.\n- **Don't chain `codegraph_search` + `codegraph_node`** when you just want context \u2014 `codegraph_context` is one round-trip.\n- **Don't use `codegraph_explore` for narrow questions** \u2014 it's a multi-call deep dive, expensive in tokens. Save it for genuine \"I'm new here\" surveys.\n- **Don't query the index immediately after editing a file** \u2014 the watcher needs ~500ms to debounce + sync. Wait for the next turn.\n\n## Limitations\n\n- Index lags file writes by ~1 second.\n- Cross-file resolution is best-effort name matching; ambiguous calls may return multiple candidates.\n- No live correctness validation \u2014 that's still the TypeScript compiler / test suite / linter's job. Codegraph supplements those with structural context they don't have.\n";
+export declare const SERVER_INSTRUCTIONS = "# Codegraph \u2014 code intelligence over an indexed knowledge graph\n\nCodegraph is a SQLite knowledge graph of every symbol, edge, and file\nin the workspace. Reads are sub-millisecond; the index lags writes by\nabout a second through the file watcher. Consult it BEFORE writing or\nediting code, not during.\n\n## Answer directly \u2014 don't delegate exploration\n\nFor \"how does X work\", architecture, trace, or where-is-X questions,\nanswer DIRECTLY using 2-3 codegraph calls: `codegraph_context` first,\nthen ONE `codegraph_explore` for the source of the symbols it surfaces.\nCodegraph IS the pre-built search index \u2014 so delegating the lookup to a\nseparate file-reading sub-task/agent, or running your own grep + read\nloop, repeats work codegraph already did and costs more for the same\nanswer. Reach for raw Read/Grep only to confirm a specific detail\ncodegraph didn't cover. A direct codegraph answer is typically a handful\nof calls; a grep/read exploration is dozens.\n\n## Tool selection by intent\n\n- **\"What is the symbol named X?\"** \u2192 `codegraph_search`\n- **\"What's the deal with this task / feature / area?\"** \u2192 `codegraph_context` (PRIMARY \u2014 composes search + node + callers + callees in one call)\n- **\"What calls this?\"** \u2192 `codegraph_callers`\n- **\"What does this call?\"** \u2192 `codegraph_callees`\n- **\"What would changing this break?\"** \u2192 `codegraph_impact`\n- **\"Show me this symbol's source / signature / docstring.\"** \u2192 `codegraph_node`\n- **\"Show me several related symbols' source / survey an area.\"** \u2192 `codegraph_explore` (ONE capped call; prefer over many codegraph_node/Read)\n- **\"What's in directory X?\"** \u2192 `codegraph_files`\n- **\"Is the index ready / what's its size?\"** \u2192 `codegraph_status`\n\n## Common chains\n\n- **Onboarding**: `codegraph_context` first. If still unclear, `codegraph_explore` for breadth, then `codegraph_node` on specific symbols.\n- **Refactor planning**: `codegraph_search` \u2192 `codegraph_callers` \u2192 `codegraph_impact`. The blast-radius answer comes from impact, not from walking callers manually.\n- **Debugging a regression**: `codegraph_callers` of the suspected symbol; widen with `codegraph_impact` if an unexpected call appears.\n\n## Anti-patterns\n\n- **Don't grep first** when looking up a symbol by name \u2014 `codegraph_search` is faster and returns kind + location + signature.\n- **Don't chain `codegraph_search` + `codegraph_node`** when you just want context \u2014 `codegraph_context` is one round-trip.\n- **Don't loop `codegraph_node` over many symbols** \u2014 one `codegraph_explore` call returns them all grouped by file, while each separate call re-reads the whole context and costs far more. Use `codegraph_node` for a single symbol.\n- **Don't query the index immediately after editing a file** \u2014 the watcher needs ~500ms to debounce + sync. Wait for the next turn.\n\n## Limitations\n\n- Index lags file writes by ~1 second.\n- Cross-file resolution is best-effort name matching; ambiguous calls may return multiple candidates.\n- No live correctness validation \u2014 that's still the TypeScript compiler / test suite / linter's job. Codegraph supplements those with structural context they don't have.\n";
 //# sourceMappingURL=server-instructions.d.ts.map

package/dist/mcp/server-instructions.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"server-instructions.d.ts","sourceRoot":"","sources":["../../src/mcp/server-instructions.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AACH,eAAO,MAAM,mBAAmB,wtGAiD/B,CAAC"}

package/dist/mcp/server-instructions.js

@@ -25,6 +25,18 @@ in the workspace. Reads are sub-millisecond; the index lags writes by
 about a second through the file watcher. Consult it BEFORE writing or
 editing code, not during.
 
+## Answer directly — don't delegate exploration
+
+For "how does X work", architecture, trace, or where-is-X questions,
+answer DIRECTLY using 2-3 codegraph calls: \`codegraph_context\` first,
+then ONE \`codegraph_explore\` for the source of the symbols it surfaces.
+Codegraph IS the pre-built search index — so delegating the lookup to a
+separate file-reading sub-task/agent, or running your own grep + read
+loop, repeats work codegraph already did and costs more for the same
+answer. Reach for raw Read/Grep only to confirm a specific detail
+codegraph didn't cover. A direct codegraph answer is typically a handful
+of calls; a grep/read exploration is dozens.
+
 ## Tool selection by intent
 
 - **"What is the symbol named X?"** → \`codegraph_search\`
@@ -33,7 +45,7 @@ editing code, not during.
 - **"What does this call?"** → \`codegraph_callees\`
 - **"What would changing this break?"** → \`codegraph_impact\`
 - **"Show me this symbol's source / signature / docstring."** → \`codegraph_node\`
-- **"Survey an unfamiliar topic / pattern / module."** → \`codegraph_explore\` (heavier; deep dive)
+- **"Show me several related symbols' source / survey an area."** → \`codegraph_explore\` (ONE capped call; prefer over many codegraph_node/Read)
 - **"What's in directory X?"** → \`codegraph_files\`
 - **"Is the index ready / what's its size?"** → \`codegraph_status\`
 
@@ -47,7 +59,7 @@ editing code, not during.
 
 - **Don't grep first** when looking up a symbol by name — \`codegraph_search\` is faster and returns kind + location + signature.
 - **Don't chain \`codegraph_search\` + \`codegraph_node\`** when you just want context — \`codegraph_context\` is one round-trip.
-- **Don't use \`codegraph_explore\` for narrow questions** — it's a multi-call deep dive, expensive in tokens. Save it for genuine "I'm new here" surveys.
+- **Don't loop \`codegraph_node\` over many symbols** — one \`codegraph_explore\` call returns them all grouped by file, while each separate call re-reads the whole context and costs far more. Use \`codegraph_node\` for a single symbol.
 - **Don't query the index immediately after editing a file** — the watcher needs ~500ms to debounce + sync. Wait for the next turn.
 
 ## Limitations

package/dist/mcp/server-instructions.js.map

@@ -1 +1 @@
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+{"version":3,"file":"server-instructions.js","sourceRoot":"","sources":["../../src/mcp/server-instructions.ts"],"names":[],"mappings":";;;AAAA;;;;;;;;;;;;;;;;GAgBG;AACU,QAAA,mBAAmB,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAiDlC,CAAC"}