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__/mcp-initialize.test.ts

@@ -154,4 +154,30 @@ describe('MCP initialize handshake (issue #172)', () => {
     expect(json.id).toBe(0);
     expect(json.result.serverInfo.name).toBe('codegraph');
   }, 20000);
+
+  it('answers resources/list and prompts/list with empty lists, not -32601 (issue #621)', async () => {
+    child = spawnServer(tempDir);
+    const events = tagStreams(child);
+    sendInitialize(child, tempDir);
+    await waitFor(events, (e) => e.stream === 'stdout', 5000); // initialize reply
+
+    child.stdin.write(JSON.stringify({ jsonrpc: '2.0', id: 1, method: 'resources/list', params: {} }) + '\n');
+    child.stdin.write(JSON.stringify({ jsonrpc: '2.0', id: 2, method: 'prompts/list', params: {} }) + '\n');
+
+    const replyFor = async (id: number) => {
+      const ev = await waitFor(events, (e) => {
+        if (e.stream !== 'stdout') return false;
+        try { return JSON.parse(e.text).id === id; } catch { return false; }
+      }, 5000);
+      return JSON.parse(ev.text);
+    };
+
+    const resources = await replyFor(1);
+    expect(resources.error).toBeUndefined();
+    expect(resources.result.resources).toEqual([]);
+
+    const prompts = await replyFor(2);
+    expect(prompts.error).toBeUndefined();
+    expect(prompts.result.prompts).toEqual([]);
+  }, 15000);
 });