refactor: rename persistence -> platform_store + v1 cleanup (#599 PR3/3)

## Summary
Final PR (3 of 3) for #599. Renames the slim control-plane store to its real
role, refreshes CLAUDE.md, and removes the last v1 stragglers.

- git mv codeframe/persistence -> codeframe/platform_store; updated all 31
  imports across codeframe/, tests/, scripts/, plus CI yaml + active docs
  (CONTRIBUTING.md, PRD.md, TESTING.md) and the embedded Python in
  tests/e2e/global-setup.ts (caught by codex).
- CLAUDE.md: dropped stale codeframe/server/ references (Legacy rule + repo-
  structure tree line); refreshed tests/agents/ note now that only
  dependency_resolver remains.
- Stragglers: removed orphan sample_project_config fixture, deleted the 5
  remaining #597-era v1 tests, un-ignored and fixed tests/api/test_health_endpoint.py
  (live /health coverage restored), emptied root collect_ignore.
- Pre-existing PR2 leftovers caught by CodeRabbit: deleted
  tests/blockers/test_blocker_expiration_simple.py and
  tests/lib/test_metrics_tracker.py (both referenced removed Database methods
  / dropped tables; both deselected by -m v2, so prior CI green was misleading).

## Validation
- Tests: pytest -m v2 green (2824 passed); Backend + Frontend CI green
- Lint/Type: ruff + mypy clean (181 files); CI Code Quality green
- Collect: pytest --collect-only clean (3424); zero active references to
  codeframe.persistence remain
- Boot: TestClient /health -> 200
- Cross-family review: codex (1 P2 fixed) + CodeRabbit (2 inline Major fixed)
- claude-bot advisory: 4 minor (3 fixed, 1 partly rebutted -- the
  flagged "dead" Database guard in tests/ui/conftest.py is actually used by
  the running_server fixture; simplified to a direct import)
- Demo: all 12 PR3 + 9 cumulative #599 acceptance criteria verified

## Cumulative -- #599 fully complete across PRs #602 + #603 + #604
- [x] No legacy multi-agent classes remain (PR1)
- [x] core/project.py + dead dirs removed (PR1)
- [x] Database exposes only control-plane methods (PR2)
- [x] persistence -> platform_store rename + CLAUDE.md (PR3)
- [x] codeframe serve boots (every PR)
- [x] pytest --collect-only clean; pytest -m v2 green (every PR)
- [x] cf --help + golden path; ruff + mypy clean (every PR)
- [x] Plan engine kept (verified live via engine_registry -> BuiltinPlanAdapter)

Closes #599.

Author: frankbria

.github/workflows/test.yml

@@ -331,7 +331,7 @@ jobs:
         run: |
           mkdir -p .codeframe
           source .venv/bin/activate
-          python -c "from codeframe.persistence.database import Database; db = Database('.codeframe/state.db'); db.initialize(); db.close()"
+          python -c "from codeframe.platform_store.database import Database; db = Database('.codeframe/state.db'); db.initialize(); db.close()"
           echo "✅ Database initialized"
 
       - name: Start FastAPI server in background
@@ -466,7 +466,7 @@ jobs:
   #         # E2E tests expect database at tests/e2e/.codeframe/state.db
   #         mkdir -p tests/e2e/.codeframe
   #         source .venv/bin/activate
-  #         python -c "from codeframe.persistence.database import Database; db = Database('tests/e2e/.codeframe/state.db'); db.initialize(); db.close()"
+  #         python -c "from codeframe.platform_store.database import Database; db = Database('tests/e2e/.codeframe/state.db'); db.initialize(); db.close()"
   #         echo "✅ Database initialized at tests/e2e/.codeframe/state.db"
   #
   #     - name: Start backend server
@@ -621,7 +621,7 @@ jobs:
   #       run: |
   #         mkdir -p .codeframe
   #         source .venv/bin/activate
-  #         python -c "from codeframe.persistence.database import Database; db = Database('.codeframe/state.db'); db.initialize(); db.close()"
+  #         python -c "from codeframe.platform_store.database import Database; db = Database('.codeframe/state.db'); db.initialize(); db.close()"
   #         echo "✅ Database initialized"
   #
   #     - name: Start backend server

CLAUDE.md

@@ -74,10 +74,7 @@ Golden Path commands must work from the CLI with **no server running**. FastAPI
 
 This separation prevents duplicate state transitions (e.g., DONE→DONE errors).
 
-### 4) Legacy can be read, not depended on
-`server/` is reference only. Do NOT import legacy UI/server modules into core.
-
-### 5) Keep commits runnable
+### 4) Keep commits runnable
 At all times: `codeframe --help` works, Golden Path stubs can run, no breaking renames/moves.
 
 ---
@@ -89,7 +86,6 @@ At all times: `codeframe --help` works, Golden Path stubs can run, no breaking r
 - **CLI-first**: Golden Path works **without any running FastAPI server**
 - **Adapters**: LLM providers in `codeframe/adapters/llm/`
 - **Server/UI optional**: FastAPI and UI are thin adapters over core; web UI connects via REST/WebSocket
-- `server/` contains v1 code retained as reference only; do not build toward v1 patterns
 
 ### Phase 3 Web UI (actively developed — not legacy)
 Next.js 16 App Router, TypeScript, Shadcn/UI, Tailwind CSS, Hugeicons, XTerm.js, WebSocket + SSE.
@@ -128,14 +124,15 @@ codeframe/
 │   ├── server.py, models.py, dependencies.py
 │   └── routers/    # 16 v2 router modules
 ├── auth/           # API key service + auth dependencies
-├── lib/            # rate_limiter.py, audit_logger.py
-└── server/         # Legacy v1 (reference only)
+├── lib/            # rate_limiter.py, audit_logger.py, metrics_tracker.py
+└── platform_store/ # Control-plane store: auth, api keys, audit logs,
+                    # interactive sessions, token usage (slim Database + repos)
 
 web-ui/             # Phase 3 Web UI (Next.js, actively developed)
 tests/
 ├── core/           # Core module tests (auto-marked v2)
 ├── adapters/       # LLM + E2B adapter tests
-├── agents/         # Worker agent tests
+├── agents/         # dependency_resolver tests
 ├── integration/    # Cross-module integration tests
 ├── lifecycle/      # End-to-end lifecycle tests (CLI + API + web, uses MockProvider)
 └── ui/             # FastAPI router tests

CONTRIBUTING.md

@@ -67,7 +67,7 @@ When creating new API endpoints that access project resources:
 
 ```python
 from fastapi import HTTPException, Depends
-from codeframe.persistence.database import Database
+from codeframe.platform_store.database import Database
 from codeframe.ui.dependencies import get_db, get_current_user, User
 
 @router.get("/api/projects/{project_id}/resource")

PRD.md

@@ -129,7 +129,7 @@ High‑level architecture is defined in [`specs/CODEFRAME_SPEC.md`](specs/CODEFR
 - **CLI** (`codeframe/cli.py`) – project initialization, server start, session commands.
 - **Backend API** (`codeframe/ui/server.py`) – projects, agents, tasks, blockers, discovery, PRD, context, session.
 - **Agent layer** (`codeframe/agents/*`) – lead + worker agents + pool + dependency resolver.
-- **Persistence** (`codeframe/persistence/database.py`) – all state with flattened v1.0 schema.
+- **Platform store** (`codeframe/platform_store/database.py`) – all state with flattened v1.0 schema.
 - **Context & session** (`codeframe/lib/context_manager.py`, `codeframe/core/session_manager.py`).
 - **Dashboard** (`web-ui/*`) – React/TypeScript UI with SWR and WebSocket integration.
 
@@ -219,7 +219,7 @@ This section captures the **stepwise workflows**; the next section defines forma
 
 2. DB keeps issues/tasks plus DAG dependencies; implementation lives in:
 
-   - `codeframe/persistence/database.py` methods for issues, tasks, `task_dependencies`.
+   - `codeframe/platform_store/database.py` methods for issues, tasks, `task_dependencies`.
    - `tests/api/test_api_issues.py` verifies the contract.
 
 3. API and UI:
@@ -264,7 +264,7 @@ This section captures the **stepwise workflows**; the next section defines forma
 1. When blocked, worker agents create blockers in DB:
 
    - Schema and behavior in `specs/049-human-in-loop/spec.md`.
-   - Implementation in `codeframe/persistence/database.py` and `codeframe/ui/server.py` endpoints:
+   - Implementation in `codeframe/platform_store/database.py` and `codeframe/ui/server.py` endpoints:
      - `GET /api/projects/{id}/blockers`
      - `GET /api/blockers/{id}`
      - `POST /api/blockers/{id}/resolve`

TESTING.md

@@ -70,7 +70,7 @@
 #### 2.2 Agent Creation
 - [ ] Use Python REPL or script:
   ```python
-  from codeframe.persistence.database import Database
+  from codeframe.platform_store.database import Database
   db = Database("test-project/.codeframe/state.db")
   db.initialize()
   agent_id = db.create_agent("lead-1", "lead", "claude", "directive")
@@ -123,7 +123,7 @@
 - [ ] Test Lead Agent initialization:
   ```python
   from codeframe.agents.lead_agent import LeadAgent
-  from codeframe.persistence.database import Database
+  from codeframe.platform_store.database import Database
 
   db = Database("test-project/.codeframe/state.db")
   db.initialize()
@@ -190,7 +190,7 @@
 - [ ] Test agent lifecycle:
   ```python
   from codeframe.agents.lead_agent import LeadAgent
-  from codeframe.persistence.database import Database
+  from codeframe.platform_store.database import Database
   from codeframe.core.models import AgentMaturity
 
   db = Database("test-project/.codeframe/state.db")

codeframe/auth/api_key_router.py

@@ -23,7 +23,7 @@
     SCOPE_WRITE,
 )
 from codeframe.core.api_key_service import ApiKeyService
-from codeframe.persistence.database import Database
+from codeframe.platform_store.database import Database
 
 logger = logging.getLogger(__name__)
 

codeframe/auth/dependencies.py

@@ -183,7 +183,7 @@ async def get_api_key_auth(
             # Fallback: create database connection
             logger.warning("No db in app.state, creating fallback connection for API key auth")
             import os
-            from codeframe.persistence.database import Database
+            from codeframe.platform_store.database import Database
 
             db_path = os.getenv(
                 "DATABASE_PATH",

codeframe/cli/auth_commands.py

@@ -41,7 +41,7 @@
     CredentialSource,
 )
 from codeframe.core.api_key_service import ApiKeyService
-from codeframe.persistence.database import Database
+from codeframe.platform_store.database import Database
 
 logger = logging.getLogger(__name__)
 

codeframe/cli/stats_commands.py

@@ -45,7 +45,7 @@ def _get_db():
     Raises:
         typer.Exit: If no workspace is found.
     """
-    from codeframe.persistence.database import Database
+    from codeframe.platform_store.database import Database
 
     db_path = Path(".codeframe/state.db")
     if not db_path.exists():

codeframe/core/api_key_service.py

@@ -15,7 +15,7 @@
     SCOPE_READ,
     SCOPE_WRITE,
 )
-from codeframe.persistence.database import Database
+from codeframe.platform_store.database import Database
 
 logger = logging.getLogger(__name__)