conductor(track): Initialize mcp_architecture_refactor_20260606

Track + metadata + state + tracks.md registration for the 2,205-line
mcp_client.py split into a slim controller + 6 native sub-MCPs + 1
external sub-MCP.

Key design decisions (per user feedback):
- Naming convention: mcp_<type>.py for native MCPs (mcp_file_io.py,
  mcp_python.py, mcp_c.py, mcp_cpp.py, mcp_web.py, mcp_analysis.py).
- ExternalMCPManager class name preserved (moves to mcp_external.py).
- Sub-MCP shape: class with name / description / tools / invoke().
- MCPController: holds ALL_SUB_MCPS list, inverted-dict tool lookup,
  3-layer security (extracted to mcp_client_security.py), schema
  aggregation.
- Each invoke() returns Result[str, ErrorInfo] (from
  data_oriented_error_handling_20260606).
- Backward compat: mcp_client_legacy.py re-exports all 45+ old
  symbols; the 4 existing test files + src/app_controller.py:61
  direct call continue to work.

DSL future (per user notes on APL/K/Cosy): NOT in this track.
Documented in spec §12.1 as the mcp_dsl_20260606 follow-up.
Sub-MCP architecture is the natural unit to pair with a DSL emitter.

7 phases. ~22 task slots. New tests: 9 (one per sub-MCP + controller +
security + legacy). Modified tests: 4 (existing mcp_* tests must
pass unchanged).

Blocked by: data_oriented_error_handling_20260606, data_structure_strengthening_20260606.
Blocks: mcp_dsl_20260606 (future DSL track).

conductor/tracks.md

@@ -173,6 +173,10 @@ User review surfaced five outstanding UI issues, each previously attempted witho
    *Link: [./tracks/data_structure_strengthening_20260606/](./tracks/data_structure_strengthening_20260606/), Spec: [./tracks/data_structure_strengthening_20260606/spec.md](./tracks/data_structure_strengthening_20260606/spec.md), Plan: [./tracks/data_structure_strengthening_20260606/plan.md](./tracks/data_structure_strengthening_20260606/plan.md) (to be authored by writing-plans skill)*
    *Goal: Improve AI-readability by naming 430 currently-anonymous `dict[str, Any]` / `list[dict[...]]` / `Tuple[...]` types. New `src/type_aliases.py` with 10 `TypeAlias` definitions (`Metadata`, `CommsLogEntry`, `CommsLog`, `HistoryMessage`, `History`, `FileItem`, `FileItems`, `ToolDefinition`, `ToolCall`, `CommsLogCallback`) and 1 `NamedTuple` (`FileItemsDiff`). Mechanical replacement of 345 weak sites across 6 high-traffic files: `src/ai_client.py` (139), `src/app_controller.py` (86), `src/models.py` (51), `src/api_hook_client.py` (32), `src/project_manager.py` (20), `src/aggregate.py` (17). Add `--strict` mode to the existing `scripts/audit_weak_types.py` (committed in 84fd9ac9; found the 430 sites) so it becomes a permanent CI gate that fails when new weak types are introduced. Generate `scripts/audit_weak_types.baseline.json` with the post-refactor count. 2 phases: aliases + 6-file replacement + audit baseline; NamedTuples + docs + archive. **Data-grounded**: the audit script is the source of truth; the count drops from 430 to ~60 (86% reduction) in the 6 high-traffic files. **Honest about what's missing**: 23 lower-impact files remain; TypedDict/dataclass migration is deferred to a follow-up track. 2-3 days work, 1-2 phases, low risk.*
 
+0g. [ ] **Track: MCP Architecture Refactor (Sub-MCP Extraction)** `[track-created: <pending>]`
+   *Link: [./tracks/mcp_architecture_refactor_20260606/](./tracks/mcp_architecture_refactor_20260606/), Spec: [./tracks/mcp_architecture_refactor_20260606/spec.md](./tracks/mcp_architecture_refactor_20260606/spec.md), Plan: [./tracks/mcp_architecture_refactor_20260606/plan.md](./tracks/mcp_architecture_refactor_20260606/plan.md) (to be authored by writing-plans skill)*
+   *Goal: Split the 2,205-line monolithic `src/mcp_client.py` (45 module-level functions) into a slim controller + 6 native sub-MCPs + 1 external sub-MCP. Naming convention `mcp_<type>.py` for native MCPs: `mcp_file_io.py` (9 tools), `mcp_python.py` (14), `mcp_c.py` (5), `mcp_cpp.py` (5), `mcp_web.py` (2), `mcp_analysis.py` (2). The existing `ExternalMCPManager` is extracted to `mcp_external.py` (class name preserved). New `MCPController` class in `src/mcp_client.py` holds the 3-layer security model (extracted to `src/mcp_client_security.py`), the `ALL_SUB_MCPS` registration list, and the inverted-dict dispatch lookup. New `src/mcp_client_legacy.py` re-exports all 45+ old symbols for backward compat (the 4 existing test files + `src/app_controller.py:61` continue to work). Each sub-MCP's `invoke()` returns `Result[str, ErrorInfo]` (Fleury pattern). Path parameters use the `Metadata` family aliases. **Blocked by** `data_oriented_error_handling_20260606` (for `Result`/`ErrorInfo`) and `data_structure_strengthening_20260606` (for `Metadata` aliases). 7 phases: foundation (security + controller), move-to-legacy, extract File I/O, extract Python, extract C/C++/Web/Analysis, extract External, dispatch update + docs + archive. **Out of scope** (per user): a per-MCP DSL (APL/K/Cosy-inspired) for compact tool calls — deferred to `mcp_dsl_20260606` follow-up. JSON-only for now.*
+
 0b. [x] **Track: rag_phase4_stress_test_flake_20260606** — fixed 16412ad5
    *Status: 2026-06-06 — Surfaced during post-v2 verification. Resolved: real bug, NOT a test flake. Root cause: ChromaDB collection dimension mismatch across test runs. The persistent on-disk collection (`tests/artifacts/live_gui_workspace/.slop_cache/chroma_test_stress/`) was created by a previous run with Gemini embeddings (3072-dim); the current run uses local SentenceTransformers (384-dim). `index_file()` upserts silently corrupt the collection, then `search()` fails with `Collection expecting embedding with dimension of 3072, got 384` and the AI request never reaches 'done' status, timing out the 50*0.5s = 25s poll loop. Fix: `RAGEngine._init_vector_store` now calls `_validate_collection_dim` which inspects the first existing vector's dim, compares to the current provider's output, and recreates the collection on mismatch (with a stderr warning). Regression tests added: `test_rag_collection_dim_mismatch_recreates_collection` and `test_rag_collection_dim_match_preserves_collection` in `tests/test_rag_engine.py`. This also fixes a real user-facing bug: switching embedding providers in the GUI previously caused silent corruption. Commit 16412ad5.*
 0a. [ ] **Track: prior_session_test_harden_20260605** [superseded by live_gui_test_hardening_v2_20260605]