docs: complete MCP Phase 1, mark all parts merged

All 6 parts of MCP Phase 1 Tools Improvement are complete:
- 1.1: Pure pattern extractors
- 1.2: Index-based analysis (10-30x faster)
- 1.3: Dead code cleanup
- 1.4: Agent usability (merge health, rename params, JSON, suggestions)
- 1.5: AST pattern analysis (tree-sitter queries)
- 1.6: Graph algorithms (PageRank, components, shortest path)

File importance ranking inspired by aider's repo map
(https://github.com/Aider-AI/aider).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: prosdev

.claude/da-plans/README.md

@@ -11,7 +11,7 @@ Implementation deviations are logged at the bottom of each plan file.
 |-------|-------------|--------|
 | [Core](core/) | Scanner, vector storage, services, indexer | Phase 1: Merged, Phase 2: Merged (indexing rethink) |
 | [CLI](cli/) | Command-line interface | Not started |
-| [MCP Server](mcp/) | Model Context Protocol server + adapters | Phase 1: Draft (tools improvement) |
+| [MCP Server](mcp/) | Model Context Protocol server + adapters | Phase 1: Merged (tools improvement) |
 | [Subagents](subagents/) | Coordinator, explorer, planner, GitHub agents | Not started |
 | [Integrations](integrations/) | Claude Code, VS Code, Cursor | Not started |
 | [Logger](logger/) | @prosdevlab/kero centralized logging | Not started |

.claude/da-plans/mcp/phase-1-mcp-tools-improvement/overview.md

@@ -1,6 +1,6 @@
 # Phase 1: MCP Tools Improvement
 
-**Status:** In progress (Parts 1.1–1.5 merged, 1.6 in progress)
+**Status:** Complete (all parts merged)
 
 ## Context