Code Graph RAG: symlinks let analyzed repositories read and overwrite outside files

Code Graph RAG is an AI-powered knowledge graph and retrieval system for querying, understanding, and editing multi-language codebases. Prior to 0.0.589, AstGrepService in codebase_rag/tools/ast_grep_service.py enumerates files beneath project_root and relies on should_skip_path in codebase_rag/utils/path_utils.py to classify them, but the containment check operates on unresolved lexical paths. A symbolic link planted inside an analyzed repository can therefore reference a file outside the configured root while still appearing in scope. The structural_search tool follows the link and discloses readable content without an approval gate, while structural_replace with dry_run=False follows it and overwrites writable content; the MCP path invokes structural replacement without the agent-loop approval control. An attacker who causes a victim to analyze a repository containing such a link can read credentials, keys, environment files, or sibling source and can modify files accessible to the code-graph-rag process. This issue is fixed in version 0.0.589.