Tool Optimizations & Linked Issues Detection + CI/CD Pipelining

[BurakKTopal]

Tool Optimizations & Linked Issues Detection

This PR consolidates and optimizes the CTM tooling, adds automatic origin detection, and fixes linked issue detection via GraphQL.

Key Changes

Tool Consolidation (35 → 32 tools)

• Merged pickaxe_search into get_local_line_context for automatic origin detection
• Merged explain_directory into list_github_tree via include_activity parameter
• Merged get_recent_activity into get_activity_summary with path filtering
• Removed redundant get_code_context (functionality in get_line_context)

Automatic Origin Detection

• get_local_line_context now auto-detects when code was first introduced using pickaxe
• Distinguishes between "last modified" (blame) and "origin" (first introduction)
• Follows file renames to find true origin even after refactoring
• Strips comment markers to find origin even if comment style changed

Linked Issues via GraphQL

• Fixed: Issues linked via GitHub's Development sidebar are now detected
• Switched from REST Timeline API (doesn't return issue numbers) to GraphQL closingIssuesReferences
• PR number is filtered from issue_numbers to avoid false positives

Agent Improvements

• Added html_url and pr_url to all commit responses for reliable linking
• Updated system prompt to prevent URL construction errors (use provided URLs)
• Removed emojis from console logs
• Multi-tab support in VSCode extension

Caching Enhancements

• GraphQL linked issues cached with 1-hour TTL
• File rename chains cached for faster repeated lookups

Files Changed

Area	Files
MCP Server	stdio_server.py, github_client.py, cache.py, git_repo.py
VSCode Extension	agent.ts, factStore.ts, contextPanel.ts, extension.ts
Documentation	README.md, CLAUDE.md, SYSTEM_PROMPT.md

Test Plan

• Verify get_local_line_context returns origin field with true introduction commit
• Test linked issues detection on PR with Development sidebar links
• Confirm list_github_tree with include_activity=true returns contributor info
• Check pickaxe_search follows file renames correctly
• Verify all tool responses include html_url for commits