feat: zero-config indexing driven by .gitignore (#283) (#285)

Remove .codegraph/config.json and the entire config surface. CodeGraph now
indexes every file whose extension maps to a supported language and respects
.gitignore everywhere — git repos via git itself, non-git projects via the
`ignore` library (root + nested .gitignore files, the same way git does).

- Remove CodeGraphConfig/DEFAULT_CONFIG, src/config.ts, and the public config
  API (the `config` option on init, getConfig/updateConfig/getConfigPath).
- Derive the source-file allowlist from EXTENSION_MAP (isSourceFile); maxFileSize
  is now a constant. Drop the .codegraphignore marker.
- Behavior change: committed, non-gitignored dirs (vendor/, a committed dist/)
  are now indexed — .gitignore is the single source of truth.

Earlier inert fields (languages, frameworks, extractDocstrings, trackCallSites,
customPatterns) and their dead helpers are removed as part of this.

Resolves #283.

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

__tests__/foundation.test.ts

@@ -9,8 +9,7 @@ import * as fs from 'fs';
 import * as path from 'path';
 import * as os from 'os';
 import { CodeGraph } from '../src';
-import { DEFAULT_CONFIG, Node, Edge } from '../src/types';
-import { loadConfig, saveConfig } from '../src/config';
+import { Node, Edge } from '../src/types';
 import { isInitialized, getCodeGraphDir, validateDirectory } from '../src/directory';
 import { DatabaseConnection, getDatabasePath } from '../src/db';
 
@@ -60,41 +59,12 @@ describe('CodeGraph Foundation', () => {
       cg.close();
     });
 
-    it('should create config.json with defaults', () => {
-      const cg = CodeGraph.initSync(tempDir);
-
-      const configPath = path.join(getCodeGraphDir(tempDir), 'config.json');
-      expect(fs.existsSync(configPath)).toBe(true);
-
-      const config = cg.getConfig();
-      expect(config.version).toBe(DEFAULT_CONFIG.version);
-      expect(config.include).toEqual(DEFAULT_CONFIG.include);
-      expect(config.exclude).toEqual(DEFAULT_CONFIG.exclude);
-
-      cg.close();
-    });
-
     it('should throw if already initialized', () => {
       const cg = CodeGraph.initSync(tempDir);
       cg.close();
 
       expect(() => CodeGraph.initSync(tempDir)).toThrow(/already initialized/i);
     });
-
-    it('should accept custom config options', () => {
-      const cg = CodeGraph.initSync(tempDir, {
-        config: {
-          maxFileSize: 500000,
-          extractDocstrings: false,
-        },
-      });
-
-      const config = cg.getConfig();
-      expect(config.maxFileSize).toBe(500000);
-      expect(config.extractDocstrings).toBe(false);
-
-      cg.close();
-    });
   });
 
   describe('Opening Projects', () => {
@@ -112,17 +82,6 @@ describe('CodeGraph Foundation', () => {
     it('should throw if not initialized', () => {
       expect(() => CodeGraph.openSync(tempDir)).toThrow(/not initialized/i);
     });
-
-    it('should preserve configuration across open/close', () => {
-      const cg1 = CodeGraph.initSync(tempDir, {
-        config: { maxFileSize: 123456 },
-      });
-      cg1.close();
-
-      const cg2 = CodeGraph.openSync(tempDir);
-      expect(cg2.getConfig().maxFileSize).toBe(123456);
-      cg2.close();
-    });
   });
 
   describe('Static Methods', () => {
@@ -182,31 +141,6 @@ describe('CodeGraph Foundation', () => {
     });
   });
 
-  describe('Configuration', () => {
-    it('should load and merge config with defaults', () => {
-      const cg = CodeGraph.initSync(tempDir);
-      cg.close();
-
-      const config = loadConfig(tempDir);
-      expect(config.version).toBe(DEFAULT_CONFIG.version);
-      expect(config.rootDir).toBe(path.resolve(tempDir));
-    });
-
-    it('should update configuration', () => {
-      const cg = CodeGraph.initSync(tempDir);
-
-      cg.updateConfig({ maxFileSize: 999999 });
-
-      expect(cg.getConfig().maxFileSize).toBe(999999);
-
-      cg.close();
-
-      // Verify persistence
-      const config = loadConfig(tempDir);
-      expect(config.maxFileSize).toBe(999999);
-    });
-  });
-
   describe('Directory Management', () => {
     it('should validate directory structure', () => {
       const cg = CodeGraph.initSync(tempDir);