Server has 5 tools with basic schemas and descriptions, but significant quality gaps. Tool names lack consistent verb-noun structure (analyze_github_repo, get_repo_info are acceptable; generate_knowledge_graph and clone_or_update_repo are weak). Descriptions are present but generic (10-100 chars, below the 50-200 char LLM-optimized baseline). Parameter descriptions are minimal or absent. No output schemas documented. No error handling guidance. No tool annotations (readOnlyHint/destructiveHint). Critical security issue: clone_or_update_repo accepts arbitrary repo_url and target_dir without validation, risking command injection and path traversal. No pagination support despite tools returning potentially large datasets.

• Document output schemas for all tools. Specify what fields are returned, their types, and which IDs/references downstream tools need. Example: analyze_codebase should return {files: [{path, classes, functions}], imports: [...], dependencies: [...]}.
• Add input validation and sanitization to clone_or_update_repo. Validate repo_url matches GitHub URL pattern (github.com/owner/repo), reject paths with ../ or absolute paths, use subprocess with shell=False.
• Expand parameter descriptions to 50-100 chars with format/constraint guidance. E.g., 'repo_url: GitHub repository URL (format: https://github.com/owner/repo)' and 'path: Local filesystem path to codebase (must exist, no symlinks to parent dirs)'.
• Add tool annotations: mark analyze_github_repo, get_repo_info, analyze_codebase as readOnlyHint=true; mark clone_or_update_repo and generate_knowledge_graph as destructiveHint=true.
• Split clone_or_update_repo into two tools: clone_repo (idempotent, creates or updates) and update_repo (updates existing only). Add error handling that guides LLM: 'Repo already exists at target_dir. Use update_repo to refresh, or choose a different target_dir.'