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>

src/db/queries.ts

@@ -1588,10 +1588,19 @@ export class QueryBuilder {
   getUnresolvedReferencesByFiles(filePaths: string[]): UnresolvedReference[] {
     if (filePaths.length === 0) return [];
 
-    const placeholders = filePaths.map(() => '?').join(',');
-    const rows = this.db
-      .prepare(`SELECT * FROM unresolved_refs WHERE file_path IN (${placeholders})`)
-      .all(...filePaths) as UnresolvedRefRow[];
+    // Chunk under SQLite's parameter limit: the first sync of a very large repo
+    // passes every changed file here, which an unbounded `IN (...)` would bind
+    // as one parameter each — exceeding MAX_VARIABLE_NUMBER and aborting with
+    // "too many SQL variables". (#540)
+    const rows: UnresolvedRefRow[] = [];
+    for (let i = 0; i < filePaths.length; i += SQLITE_PARAM_CHUNK_SIZE) {
+      const chunk = filePaths.slice(i, i + SQLITE_PARAM_CHUNK_SIZE);
+      const placeholders = chunk.map(() => '?').join(',');
+      const chunkRows = this.db
+        .prepare(`SELECT * FROM unresolved_refs WHERE file_path IN (${placeholders})`)
+        .all(...chunk) as UnresolvedRefRow[];
+      rows.push(...chunkRows);
+    }
 
     return rows.map((row) => ({
       fromNodeId: row.from_node_id,