@stupidloud/codegraph 0.7.15 → 0.8.1

package/dist/installer/targets/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/installer/targets/types.js

@@ -0,0 +1,16 @@
+"use strict";
+/**
+ * Agent target abstraction for the installer.
+ *
+ * Each MCP-capable agent (Claude Code, Cursor, Codex CLI, opencode, ...)
+ * implements this interface so the installer orchestrator can write the
+ * right MCP-server config + instructions file + permissions for that
+ * agent without baking client-specific paths into core code. Adding a
+ * new agent = one new file in `targets/` + one entry in `registry.ts`.
+ *
+ * Closes the Claude-locked installer issue (upstream #137). The
+ * runtime MCP server is already agent-agnostic; this brings the
+ * installer to the same surface.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=types.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/installer/targets/types.ts"],"names":[],"mappings":";AAAA;;;;;;;;;;;;GAYG"}

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- **\"How does X work? / trace X end to end / explain the Y system / architecture?\"** \u2192 `codegraph_explore` (PRIMARY for understanding \u2014 seed it with the key symbol names, read its output, don't grep+Read your way there)\n- **\"What is the symbol named X? / where is X defined?\"** \u2192 `codegraph_search` (pinpoint lookups)\n- **\"What's the deal with this task / feature / area?\"** \u2192 `codegraph_context` (lighter composed view of search + node + callers + callees)\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- **Understanding / onboarding**: feed `codegraph_explore` the key symbol/file names and read its output (line-numbered source from many files in one call). If the question names nothing concrete, do ONE quick `codegraph_search` / `codegraph_context` to surface the names, then explore with them. Fill remaining gaps with `codegraph_node` / Read \u2014 don't drop back to grep+Read for the whole topic.\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 search-then-Read your way through an understanding question** \u2014 feed the names you find into `codegraph_explore` instead of Reading the files one by one; it does that whole loop in one call and returns line numbers you can cite directly.\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 reach for `codegraph_explore` on a pinpoint \"where is X defined\" lookup** \u2014 `codegraph_search` is one cheap call.\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 @@
-{"version":3,"file":"server-instructions.d.ts","sourceRoot":"","sources":["../../src/mcp/server-instructions.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AACH,eAAO,MAAM,mBAAmB,s7EAqC/B,CAAC"}
+{"version":3,"file":"server-instructions.d.ts","sourceRoot":"","sources":["../../src/mcp/server-instructions.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AACH,eAAO,MAAM,mBAAmB,ymIAoD/B,CAAC"}

package/dist/mcp/server-instructions.js

@@ -25,29 +25,44 @@ 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\`
-- **"What's the deal with this task / feature / area?"** → \`codegraph_context\` (PRIMARY — composes search + node + callers + callees in one call)
+- **"How does X work? / trace X end to end / explain the Y system / architecture?"** → \`codegraph_explore\` (PRIMARY for understanding — seed it with the key symbol names, read its output, don't grep+Read your way there)
+- **"What is the symbol named X? / where is X defined?"** → \`codegraph_search\` (pinpoint lookups)
+- **"What's the deal with this task / feature / area?"** → \`codegraph_context\` (lighter composed view of search + node + callers + callees)
 - **"What calls this?"** → \`codegraph_callers\`
 - **"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\`
 
 ## Common chains
 
-- **Onboarding**: \`codegraph_context\` first. If still unclear, \`codegraph_explore\` for breadth, then \`codegraph_node\` on specific symbols.
+- **Understanding / onboarding**: feed \`codegraph_explore\` the key symbol/file names and read its output (line-numbered source from many files in one call). If the question names nothing concrete, do ONE quick \`codegraph_search\` / \`codegraph_context\` to surface the names, then explore with them. Fill remaining gaps with \`codegraph_node\` / Read — don't drop back to grep+Read for the whole topic.
 - **Refactor planning**: \`codegraph_search\` → \`codegraph_callers\` → \`codegraph_impact\`. The blast-radius answer comes from impact, not from walking callers manually.
 - **Debugging a regression**: \`codegraph_callers\` of the suspected symbol; widen with \`codegraph_impact\` if an unexpected call appears.
 
 ## Anti-patterns
 
+- **Don't search-then-Read your way through an understanding question** — feed the names you find into \`codegraph_explore\` instead of Reading the files one by one; it does that whole loop in one call and returns line numbers you can cite directly.
 - **Don't grep first** when looking up a symbol by name — \`codegraph_search\` is faster and returns kind + location + signature.
+- **Don't reach for \`codegraph_explore\` on a pinpoint "where is X defined" lookup** — \`codegraph_search\` is one cheap call.
 - **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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAoDlC,CAAC"}

package/dist/mcp/tools.d.ts

@@ -10,6 +10,47 @@ import CodeGraph from '../index';
  * but smaller ones should use fewer to avoid unnecessary overhead.
  */
 export declare function getExploreBudget(fileCount: number): number;
+/**
+ * Adaptive output budget for `codegraph_explore`, scaled to project size.
+ *
+ * Smaller codebases get a tighter total cap, fewer default files, smaller
+ * per-file cap, and tighter clustering — so a focused query on a 100-file
+ * project doesn't dump a whole file's worth of source into the agent's
+ * context. Larger codebases keep the generous defaults because the
+ * agent's native discovery cost (grep + find + many Reads) genuinely
+ * dwarfs a fat explore call at that scale.
+ *
+ * Meta-text (relationships map, "additional relevant files" list,
+ * completeness signal, budget note) is gated off for tiny projects
+ * where one rich call is the whole story and the extra prose is just
+ * overhead.
+ *
+ * Tier breakpoints mirror `getExploreBudget` so a project sits in the
+ * same tier across both knobs.
+ */
+export interface ExploreOutputBudget {
+    /** Hard cap on total output characters. */
+    maxOutputChars: number;
+    /** Default `maxFiles` when the caller didn't specify one. */
+    defaultMaxFiles: number;
+    /** Cap on contiguous source returned per file (across all its clusters). */
+    maxCharsPerFile: number;
+    /** Cluster gap threshold in lines — tighter clustering on small projects. */
+    gapThreshold: number;
+    /** Max symbols listed in the per-file header (`#### path — sym(kind), ...`). */
+    maxSymbolsInFileHeader: number;
+    /** Max edges shown per relationship kind in the Relationships section. */
+    maxEdgesPerRelationshipKind: number;
+    /** Include the "Relationships" section. */
+    includeRelationships: boolean;
+    /** Include the "Additional relevant files (not shown)" trailing list. */
+    includeAdditionalFiles: boolean;
+    /** Include the "Complete source code is included above…" reminder. */
+    includeCompletenessSignal: boolean;
+    /** Include the explore-budget reminder at the end. */
+    includeBudgetNote: boolean;
+}
+export declare function getExploreOutputBudget(fileCount: number): ExploreOutputBudget;
 /**
  * MCP Tool definition
  */
@@ -56,11 +97,17 @@ export declare const tools: ToolDefinition[];
 export declare class ToolHandler {
     private cg;
     private projectCache;
+    private defaultProjectHint;
     constructor(cg: CodeGraph | null);
     /**
      * Update the default CodeGraph instance (e.g. after lazy initialization)
      */
     setDefaultCodeGraph(cg: CodeGraph): void;
+    /**
+     * Record the directory the server tried to resolve the default project from.
+     * Used only to make the "no default project" error actionable.
+     */
+    setDefaultProjectHint(searchedPath: string): void;
     /**
      * Whether a default CodeGraph instance is available
      */
@@ -117,14 +164,16 @@ export declare class ToolHandler {
      * Handle codegraph_impact
      */
     private handleImpact;
-    /** Maximum output for explore tool — sized to stay under MCP client token limits (~10k tokens) */
-    private static readonly EXPLORE_MAX_OUTPUT;
     /**
      * Handle codegraph_explore — deep exploration in a single call
      *
      * Strategy: find relevant symbols via graph traversal, group by file,
      * then read contiguous file sections covering all symbols per file.
      * This replaces multiple codegraph_node + Read calls.
+     *
+     * Output size is adaptive to project file count via
+     * `getExploreOutputBudget` — see #185 for why a fixed 35k cap was a
+     * tax on small projects while earning its keep on large ones.
      */
     private handleExplore;
     /**
@@ -160,9 +209,22 @@ export declare class ToolHandler {
      * Returns the best match and a note about alternatives if any.
      */
     /**
-     * Check if a node matches a symbol query, supporting both simple names and
-     * qualified "Parent.child" notation (e.g., "Session.request" matches a method
-     * named "request" inside a class named "Session").
+     * Check if a node matches a symbol query.
+     *
+     * Accepts simple names (`run`) and three flavors of qualifier:
+     *   - dotted     `Session.request`         (TS/JS/Python)
+     *   - colon-pair `stage_apply::run`        (Rust, C++, Ruby)
+     *   - slash      `configurator/stage_apply` (path-ish)
+     *
+     * Multi-level qualifiers compose: `crate::configurator::stage_apply::run`
+     * works. Rust path prefixes (`crate`, `super`, `self`) are stripped so
+     * the canonical `crate::module::symbol` form resolves.
+     *
+     * Resolution order, last part must always equal `node.name`:
+     *   1. Suffix-match against `qualifiedName` (handles class-scoped methods
+     *      where the extractor builds the qualified name from the AST stack)
+     *   2. File-path containment (handles file-derived modules in Rust/
+     *      Python — `stage_apply::run` matches a `run` in `stage_apply.rs`)
      */
     private matchesSymbol;
     private findSymbol;
@@ -178,6 +240,14 @@ export declare class ToolHandler {
     private formatSearchResults;
     private formatNodeList;
     private formatImpact;
+    /**
+     * Build a compact structural outline of a container symbol from its
+     * indexed children (methods, fields, properties, …) — name, kind,
+     * line number, and signature — so the agent gets the shape of a class
+     * without the full source of every method. Returns '' when the container
+     * has no indexed children, so the caller can fall back to full source.
+     */
+    private buildContainerOutline;
     private formatNodeDetails;
     private formatTaskContext;
     private textResult;

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

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