docs(implementation_plan.md): Added what was accomplished

implementation_plan.md

@@ -882,6 +882,40 @@ The following work from the previous implementation has been completed and will
 - Verification: lint 0, typecheck 0, 2630 scenarios passed, 97% total coverage. Tool builtins 97-100% coverage.
 - Branch: `feature/m1-tool-builtins` (based on `feature/m1-tool-runtime-core`)
 - 2026-02-14: Commit traceability sweep found no matching git log entries for skill schema/examples, skill CLI, provider actors, MCP config/adapter, actor compiler, or skill registry persistence; Section 2B traceability tasks remain open.
+
+**2026-02-17**: Bugfix - Unit Test and Benchmark Failures After Master Merge [Brent]
+
+- **Context**: After merging master into `feature/q0-min-coverage` (commit `7ddd99b`), full `nox` run showed 2 failing sessions: `unit_tests-3.13` (1 scenario failure) and `benchmark` (multiple benchmark failures). All other sessions (lint, format, typecheck, security_scan, dead_code, integration_tests, coverage_report) passed.
+- **Unit test failure** — `features/project_repository.feature:38` "List projects respects limit":
+  - **Root cause**: Session mismatch in `features/steps/project_repository_steps.py`. The `NamespacedProjectRepository` creates a new SQLAlchemy session via `self._session_factory()` on each method call (session-factory pattern). The test setup passed a `sessionmaker` as the factory, so each repo method got a different session. When `context.pr_session.commit()` was called, it committed a separate session that did NOT contain the flushed data from the repo's sessions. With SQLite in-memory, only 1 of 3 projects was visible when querying with `limit=2`.
+  - **Fix** (`features/steps/project_repository_steps.py:75-91`): Changed the session factory passed to the repos from `sf` (the raw `sessionmaker`) to `lambda: session` (always returns the same session instance as `context.pr_session`). This ensures `context.pr_session.commit()` commits the data flushed by the repos. The raw `sessionmaker` is still available as `context.pr_session_factory` for tests that need independent sessions (e.g., `step_pr_create_dup`).
+- **Benchmark failures** — 5 distinct issues across 7 files:
+  1. **`cli_format_bench.py`**: `ActionListFormatSuite.setup()` and `PlanStatusFormatSuite.setup()` missing `fmt` parameter. ASV passes the parameterized value to `setup()`/`teardown()` for classes with `params`. Fix: added `fmt: str` parameter to both `setup()` and `teardown()` methods. Added `# noqa: RUF012` for ASV convention `params`/`param_names` class attributes.
+  2. **`plan_model_bench.py`**: `PhaseTransitionSuite.time_can_transition_invalid` referenced `PlanPhase.APPLIED` which no longer exists (renamed to `PlanPhase.APPLY` during spec rebaseline). Fix: changed to `PlanPhase.APPLY`.
+  3. **`plan_lifecycle_persistence_bench.py`**: `TimePhaseTransitionPersisted.time_execute_transition` failed on second ASV iteration with "Invalid phase transition from execute to execute" because `setup()` transitioned the plan to execute-ready state once, but the timing method was called repeatedly. Fix: moved plan creation + strategize transitions into the timing method itself so each iteration gets a fresh plan.
+  4. **UNIQUE constraint failures** in `plan_phase_migration_bench.py`, `project_migration_bench.py`, `resource_registry_migration_bench.py`: Benchmark methods inserted rows with fixed IDs (e.g., `_make_ulid(i)` for i=0..99). ASV calls timing methods multiple times per `setup()`, so the second call hit UNIQUE constraint violations. Fix: added batch counters (`self._batch_ctr`, `self._single_ctr`) to generate unique IDs across iterations (e.g., `_make_ulid(offset + i)` where `offset = self._batch_ctr * 100`). For `ProjectLinkInsert`, expanded the resource pool from 50 to 5000 to accommodate repeated iterations.
+  5. **`uow_lifecycle_bench.py`**: `TimeUowActionPlanRoundTrip.time_create_action_and_plan_via_uow` failed with FK constraint on plan insert, even after creating and committing the action in a separate session. Root cause: SQLite in-memory `StaticPool` + `autoflush=False` caused the plan's FK check to not see the committed action across session boundaries. Fix: simplified the benchmark to reuse the pre-seeded action (`local/bench-uow-action`) created in `setup()` rather than creating a new action per iteration.
+- **Files changed** (8 files, +87/-45 lines):
+  - `features/steps/project_repository_steps.py` — session factory fix
+  - `benchmarks/cli_format_bench.py` — parameterized setup/teardown signatures + noqa
+  - `benchmarks/plan_model_bench.py` — `APPLIED` → `APPLY`
+  - `benchmarks/plan_lifecycle_persistence_bench.py` — per-iteration plan creation
+  - `benchmarks/plan_phase_migration_bench.py` — batch counters for unique IDs
+  - `benchmarks/project_migration_bench.py` — batch counters for unique IDs
+  - `benchmarks/resource_registry_migration_bench.py` — batch counters for unique IDs
+  - `benchmarks/uow_lifecycle_bench.py` — reuse pre-seeded action
+- **Verification**: All 9 nox sessions pass:
+  - lint: success
+  - format: success
+  - typecheck: success (7s)
+  - security_scan: success (6s)
+  - dead_code: success
+  - unit_tests-3.13: success (3161 scenarios, 13765 steps, 0 failures)
+  - integration_tests-3.13: success (283 tests, 0 failures)
+  - coverage_report: success (97.3%, threshold 97%)
+  - benchmark: success (all benchmarks pass)
+- **Commit**: `122af46` on `feature/q0-min-coverage` — `fix(tests): resolve unit test and benchmark failures`
+
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 ## Roadmap