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/graph/traversal.ts

@@ -521,8 +521,11 @@ export class GraphTraverser {
       }
     }
 
-    // Get all incoming edges (things that depend on this node)
-    const incomingEdges = this.queries.getIncomingEdges(nodeId);
+    // Get all incoming edges (things that depend on this node). Exclude
+    // `contains`: a container "contains" its members but does not *depend* on
+    // them, so following it upward would climb to the parent class and then
+    // re-expand every sibling member — exploding impact for a leaf symbol. (#536)
+    const incomingEdges = this.queries.getIncomingEdges(nodeId).filter((e) => e.kind !== 'contains');
     if (incomingEdges.length === 0) return;
     const sources = this.queries.getNodesByIds(incomingEdges.map((e) => e.source));