docs: sweep stale references + MCP tools improvement plan

[prosdev]

Summary

Comprehensive documentation sweep to remove stale references after Phase 2, plus a detailed plan for MCP tools improvement.

Docs Cleanup

Tool references updated:

• MCP tool count 9 → 6 (removed dev_history, dev_plan, dev_gh references from all active docs)
• Renamed dev_inspect → dev_patterns (focused on pattern analysis, removed redundant similar-files feature)
• Deleted 3 stale tool doc pages (dev-history.mdx, dev-plan.mdx, dev-github.mdx)
• Updated tool nav, config defaults (9 → 6 adapters), and prompt registry (8 → 5 prompts)

CLI commands cleaned up:

• Removed dev explore command — merged --similar-to flag into dev search
• Removed references to deleted commands: dev init, update, stats, dashboard, git, github, plan
• Fixed search threshold default (0.7 → 0) for RRF scores
• Removed misleading percentage scores from explore output
• Made search query optional when using --similar-to

Technology references updated:

• Replaced LanceDB/@xenova/transformers → Antfly/Termite throughout active docs
• Renamed vectors.lance → vectors in all code examples
• Updated ARCHITECTURE.md, PLAN.md, vector/README.md, indexer/README.md for Antfly stack
• Updated embedding model references: all-MiniLM-L6-v2 → BAAI/bge-small-en-v1.5

Agent and config updates:

• Updated .claude/agents/ (security-reviewer, quick-scout, logic-reviewer, bug-investigator) for current tools
• Updated config.ts adapter defaults from 9 to 6
• Removed 3 prompts (analyze-issue, search-github, create-plan) and updated prompt tests
• Removed dead GitHub output functions from CLI (~200 lines)
• Updated website docs: cli.mdx, configuration.mdx, quickstart.mdx, install.mdx, tools/index.mdx
• Expanded scanner default exclusions (.env*, *.min.js, *.d.ts, generated/, .terraform/, .claude/)

MCP Tools Improvement Plan

6-part plan at .claude/da-plans/mcp/phase-1-mcp-tools-improvement/ with 12 user stories. Reviewed 3x by plan-reviewer agent, all blockers resolved.

• 1.1 — Extract pure testable pattern analyzers (refactor)
• 1.2 — Index-based pattern analysis via getDocsByFilePath (10-30x faster)
• 1.3 — Cleanup: dead code removal, health adapter GitHub code removal, missing edge case tests
• 1.4 — Agent usability: merge dev_status/dev_health, add error suggestions to all adapters, rename query → filePath, add JSON output format
• 1.5 — AST-based pattern analysis via ast-grep (optional dep, regex fallback, inspired by ast-grep)
• 1.6 — PageRank file ranking for dev_map hot paths (inspired by aider's repo map)

Test plan

• pnpm build passes
• pnpm test — 1,620 tests pass, 0 failures
• dev search "error handling" — returns 10 results, no stale references
• dev search --similar-to packages/core/src/vector/antfly-store.ts — returns 7 related files
• dev map — clean output with relative paths, proper tree connectors
• dev --help — shows only current commands (no removed ones)