fix: issue-triage quick wins (extraction, MCP probes, gitignore, CJK, impact) (#654)

Batch of small, localized fixes from an open-issue triage:

- .codegraph/.gitignore now ignores everything but itself, so the database,
  daemon.pid, sockets, and logs stop showing up in git status (#492, #484)
- MCP server answers resources/list and prompts/list with empty lists instead
  of -32601, clearing scary log lines in opencode/Codex (#621)
- index SAP HANA .xsjs/.xsjslib as JavaScript (#556) and TS .mts/.cts (#366)
- visit anonymous AMD/CommonJS/IIFE wrapper bodies so their inner functions and
  calls are indexed instead of coming up empty (#528)
- batch the changed-file lookup so a huge first sync no longer hits
  "too many SQL variables" (#540)
- list files with `git ls-files -z` so non-ASCII/CJK paths survive
  core.quotepath and are no longer silently skipped (#541)
- attach Go methods on generic receivers (*T[P]) to their type (#583, RC1)
- impact no longer climbs the structural `contains` edge, so a leaf symbol
  stops dragging in its sibling methods (#536)
- README: explicit `codegraph install` step, run in a new shell (#631)

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

__tests__/extraction.test.ts

@@ -10,7 +10,7 @@ import * as path from 'path';
 import * as os from 'os';
 import { CodeGraph } from '../src';
 import { extractFromSource, scanDirectory } from '../src/extraction';
-import { detectLanguage, isLanguageSupported, getSupportedLanguages, initGrammars, loadAllGrammars } from '../src/extraction/grammars';
+import { detectLanguage, isLanguageSupported, getSupportedLanguages, initGrammars, loadAllGrammars, isSourceFile } from '../src/extraction/grammars';
 import { normalizePath } from '../src/utils';
 
 beforeAll(async () => {
@@ -4387,3 +4387,49 @@ void helperFunction(int count) {
     expect(getSupportedLanguages()).toContain('objc');
   });
 });
+
+describe('Regression: issue-specific extraction fixes', () => {
+  it('indexes inner functions of an anonymous AMD/CommonJS module wrapper (#528)', () => {
+    const code = `
+define(['dep'], function (dep) {
+  function innerHelper(x) { return x + 1; }
+  function compute(y) { return innerHelper(y); }
+  return { compute: compute };
+});
+`;
+    const result = extractFromSource('amd-module.js', code);
+    const fns = result.nodes.filter((n) => n.kind === 'function').map((n) => n.name);
+    expect(fns).toContain('innerHelper');
+    expect(fns).toContain('compute');
+  });
+
+  it('attaches Go methods on generic receivers to their type (#583)', () => {
+    const code = `
+package main
+
+type Stack[T any] struct { items []T }
+
+func (s *Stack[T]) Push(v T) { s.items = append(s.items, v) }
+func (s Stack[T]) Len() int { return len(s.items) }
+`;
+    const result = extractFromSource('stack.go', code);
+    const methods = result.nodes.filter((n) => n.kind === 'method');
+    expect(methods.find((m) => m.name === 'Push')?.qualifiedName).toBe('Stack::Push');
+    expect(methods.find((m) => m.name === 'Len')?.qualifiedName).toBe('Stack::Len');
+  });
+
+  it('indexes new module extensions: .mts/.cts (TS) and .xsjs/.xsjslib (JS) (#366, #556)', () => {
+    expect(isSourceFile('mod.mts')).toBe(true);
+    expect(isSourceFile('mod.cts')).toBe(true);
+    expect(isSourceFile('service.xsjs')).toBe(true);
+    expect(isSourceFile('lib.xsjslib')).toBe(true);
+    expect(detectLanguage('mod.mts')).toBe('typescript');
+    expect(detectLanguage('service.xsjs')).toBe('javascript');
+
+    // End-to-end: a .mts file is parsed as TS, a .xsjs file as JS.
+    const ts = extractFromSource('mod.mts', 'export function hello(): number { return 1; }');
+    expect(ts.nodes.find((n) => n.name === 'hello' && n.kind === 'function')).toBeDefined();
+    const js = extractFromSource('service.xsjs', 'function handleRequest() { return 1; }');
+    expect(js.nodes.find((n) => n.name === 'handleRequest' && n.kind === 'function')).toBeDefined();
+  });
+});