docs: align README with current CodeGraph guidance

[okbexx]

Summary

• add codegraph_explore to the manual Claude auto-allow snippet
• update the README's Global Instructions Reference so it matches the current direct-answer guidance used by the installed instructions/server instructions
• make the reference agent-agnostic instead of Claude-only

Why

The README still showed the older guidance that told agents not to call codegraph_context / codegraph_explore directly and to spawn Explore agents. Current instructions steer agents to answer directly with codegraph_context plus one codegraph_explore, avoiding redundant file-reading subagents.

Test plan

• git diff --check
• grep check confirms the stale "NEVER call codegraph_explore" / "ALWAYS spawn an Explore agent" wording is removed from README

Docs-only change; no runtime code changed.