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Implemented project configuration to disable certain MCP tools to spare tokens with the initial schema in the context
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Lines changed: 817 additions & 34 deletions

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‎README.md‎

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@@ -537,6 +537,8 @@ Four more tools (`codegraph_callees`, `codegraph_impact`, `codegraph_files`, `co
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In a workspace with no `.codegraph/` index, the server announces itself inactive and lists **no** tools — agents work normally with their built-in tools, and indexing stays your decision.
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You can hide specific MCP tools per-project via `.codegraph/config.json` (see Configuration below). Hidden tools are removed from `tools/list` and are treated as unknown if called directly.
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---
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## Library Usage
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## Configuration
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There isn't any — CodeGraph is zero-config, with **no config file** to write or
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keep in sync. Language support is automatic from the file extension; there's
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nothing to wire up per language.
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What it skips out of the box:
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- **Dependency, build, and cache directories** — `node_modules`, `vendor`,
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`dist`, `build`, `target`, `.venv`, `Pods`, `.next`, and the like across every
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[supported stack](#supported-languages) — so the graph is your code, not
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third-party noise. This holds even with no `.gitignore`.
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- **Anything in your `.gitignore`** — honored in git repos via git, and in
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non-git projects by reading `.gitignore` directly (root and nested).
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- **Files larger than 1 MB** — generated bundles, minified JS, vendored blobs.
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To keep something else out, add it to `.gitignore`. To pull a default-excluded
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directory back **in** (say you really do want a vendored dependency indexed),
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add a negation — `!vendor/`. The defaults apply uniformly, so committing a
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dependency or build directory doesn't force it into the graph; the `.gitignore`
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negation is the explicit opt-in.
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CodeGraph works out-of-the-box with defaults, while allowing optional
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project-local overrides via `.codegraph/config.json`.
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Defaults still skip dependency/build/cache directories, respect `.gitignore`,
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and ignore files larger than 1 MB.
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```json
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{
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"version": 1,
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"languages": ["typescript", "javascript"],
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"exclude": ["node_modules/**", "dist/**", "build/**", "*.min.js"],
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"frameworks": [],
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"maxFileSize": 1048576,
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"extractDocstrings": true,
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"trackCallSites": true,
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"mcp": {
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"disabledTools": ["codegraph_explore"]
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}
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}
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```
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| Option | Description | Default |
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|--------|-------------|---------|
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| `languages` | Languages to index (auto-detected if empty) | `[]` |
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| `exclude` | Glob patterns to ignore | `["node_modules/**", ...]` |
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| `frameworks` | Framework hints for better resolution | `[]` |
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| `maxFileSize` | Skip files larger than this (bytes) | `1048576` (1MB) |
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| `extractDocstrings` | Extract docstrings from code | `true` |
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| `trackCallSites` | Track call site locations | `true` |
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| `mcp.disabledTools` | MCP tool names to hide/disable for this project | `[]` |
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Example disabled tool names: `codegraph_explore`, `codegraph_context`, `codegraph_files`.
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Notes:
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- This setting is project-local only (no global override).
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- Unknown tool names are ignored (lenient behavior).
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## Telemetry
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‎__tests__/foundation.test.ts‎

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@@ -11,7 +11,10 @@ import * as os from 'os';
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import { CodeGraph } from '../src';
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import { Node, Edge } from '../src/types';
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import { isInitialized, getCodeGraphDir, validateDirectory, codeGraphDirName, isCodeGraphDataDir } from '../src/directory';
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import { Node, Edge, DEFAULT_CONFIG } from '../src/types';
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import { isInitialized, getCodeGraphDir, validateDirectory } from '../src/directory';
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import { DatabaseConnection, getDatabasePath } from '../src/db';
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import { loadConfig } from '../src/config';
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// Create a temporary directory for each test
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function createTempDir(): string {
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});
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});
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describe('Configuration', () => {
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it('should load and merge config with defaults', () => {
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const cg = CodeGraph.initSync(tempDir);
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cg.close();
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const config = loadConfig(tempDir);
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expect(config.version).toBe(DEFAULT_CONFIG.version);
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expect(config.rootDir).toBe(path.resolve(tempDir));
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});
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it('should update configuration', () => {
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const cg = CodeGraph.initSync(tempDir);
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cg.updateConfig({ maxFileSize: 999999 });
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expect(cg.getConfig().maxFileSize).toBe(999999);
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cg.close();
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// Verify persistence
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const config = loadConfig(tempDir);
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expect(config.maxFileSize).toBe(999999);
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});
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it('should persist MCP disabled tools config', () => {
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const cg = CodeGraph.initSync(tempDir);
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cg.updateConfig({
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mcp: { disabledTools: ['codegraph_explore'] },
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});
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cg.close();
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const config = loadConfig(tempDir);
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expect(config.mcp?.disabledTools).toEqual(['codegraph_explore']);
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});
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it('should reject invalid mcp.disabledTools format', () => {
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const cg = CodeGraph.initSync(tempDir);
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cg.close();
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const configPath = path.join(getCodeGraphDir(tempDir), 'config.json');
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const raw = JSON.parse(fs.readFileSync(configPath, 'utf-8')) as Record<string, unknown>;
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raw.mcp = { disabledTools: [123] };
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fs.writeFileSync(configPath, JSON.stringify(raw, null, 2));
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expect(() => loadConfig(tempDir)).toThrow(/Invalid configuration format/i);
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});
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});
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describe('Directory Management', () => {
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it('should validate directory structure', () => {
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const cg = CodeGraph.initSync(tempDir);

‎__tests__/security.test.ts‎

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@@ -14,7 +14,7 @@ import * as path from 'path';
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import * as os from 'os';
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import { FileLock, validateProjectPath, validatePathWithinRoot } from '../src/utils';
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import CodeGraph from '../src/index';
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import { ToolHandler, tools } from '../src/mcp/tools';
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import { ToolHandler, tools, filterToolsByConfig } from '../src/mcp/tools';
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import { scanDirectory, isSourceFile } from '../src/extraction';
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import { DatabaseConnection, getDatabasePath } from '../src/db';
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import { QueryBuilder } from '../src/db/queries';
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expect(result.content[0].text).toMatch(/sensitive system directory/i);
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}
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);
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it('should hide disabled tools from tool list', async () => {
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const projectWithDisabled = createTempDir();
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const srcDir = path.join(projectWithDisabled, 'src');
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fs.mkdirSync(srcDir);
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fs.writeFileSync(path.join(srcDir, 'x.ts'), 'export const x = 1;\n');
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const disabledCg = CodeGraph.initSync(projectWithDisabled, {
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config: {
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include: ['**/*.ts'],
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exclude: [],
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mcp: { disabledTools: ['codegraph_explore'] },
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},
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});
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try {
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const disabledHandler = new ToolHandler(disabledCg);
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const toolNames = disabledHandler.getTools().map(t => t.name);
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expect(toolNames).not.toContain('codegraph_explore');
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} finally {
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disabledCg.close();
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cleanupTempDir(projectWithDisabled);
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}
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});
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it('should ignore unknown disabled tool names (lenient)', () => {
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const filtered = filterToolsByConfig(tools, {
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mcp: { disabledTools: ['not_a_real_tool_name'] },
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});
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expect(filtered).toHaveLength(tools.length);
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});
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});
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describe('Atomic Writes', () => {

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