Server has 8 well-named tools with complete input schemas and descriptions. Naming follows verb_noun convention (check_, initialize_, query_, detect_, audit_, lookup_, get_, generate_). Descriptions are substantive (100-250 chars), explaining WHAT and WHEN. However, output schemas are entirely undocumented, LLMs cannot plan downstream calls or extract structured data. Error handling is present but generic (no recovery guidance). Parameters lack type constraints (enums, ranges, patterns) and some lack descriptions. No tool annotations (readOnlyHint/destructiveHint). Security validation is good (path traversal checks, no shell invocation), but no audit logging or permission gates.

• Document output schemas for all 8 tools. Example for query_codegraph: {type: 'object', properties: {results: {type: 'array', items: {type: 'object', properties: {name: {type: 'string'}, kind: {type: 'string'}, file: {type: 'string'}, line: {type: 'number'}}}, total: {type: 'number'}}}. This enables LLMs to chain results into downstream tools.
• Add enum constraints to parameters. query_codegraph.kind should be enum: ['function', 'class', 'method', 'variable', 'import']. detect_duplicates.minLines should have minimum: 1, maximum: 100. generate_refactoring_plan.issueType already has enum, apply same pattern to other free-form params.
• Add tool annotations to ListToolsRequestSchema response. Mark initialize_codegraph and generate_refactoring_plan with destructiveHint: true. Mark all read-only tools with readOnlyHint: true. This signals agent safety constraints.
• Enhance error messages with recovery guidance. Replace 'codegraph execution failed' with 'codegraph CLI not found. Install via: npm install -g codegraph, or ensure it is in PATH.' This lets agents self-correct.
• Add per-tool permission checks and audit logging. Before initialize_codegraph or generate_refactoring_plan, log caller identity, timestamp, and parameters to stderr or a structured log. Gate destructive tools behind a permission check (e.g., require 'write:codebase' scope).