fix: remove phantom state.db path and fix explain.py skip detection

[tbroadley]

Summary

• Bug fix: explain.py gated the O(1) generation skip check on state.db existing — a file Pivot never creates. This made pivot status, pivot repro -n, and pivot repro -n -e extremely slow because every dependency was re-hashed from scratch.
• Cleanup: StateDB.__init__ now accepts the state directory directly instead of a phantom state.db path. Removed get_state_db_path() — callers use get_state_dir() directly.
• Removed state.db from the .gitignore template since it was never a real file.
• Updated docs to reference state.lmdb/ instead of state.db.

Root cause

StateDB has always used LMDB (state.lmdb/ directory), but callers constructed a state.db path that was passed to the constructor, which then did db_path.parent / "state.lmdb" to find the actual storage. No code ever created a state.db file.

In explain.py, an if state_db_path.exists(): guard (added in #245) checked for this phantom file before attempting the fast generation-based skip detection. Since the file never existed, the fast path was always skipped, falling through to expensive per-file rehashing with no hash cache.

Test plan

• All 806 affected tests pass (4 skipped)
• ruff check clean
• basedpyright clean (no new errors — 19 pre-existing errors, 444 pre-existing warnings unchanged)

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Fixes a major performance regression where pivot status / pivot repro -n / pivot repro -n -e always missed the O(1) generation-based skip path due to checking for a non-existent state.db file, and cleans up the codebase to consistently treat state as an LMDB directory (state.lmdb/) under a state directory.

Changes:

• Refactor StateDB to accept a state_dir directly and remove get_state_db_path() in favor of get_state_dir().
• Update explain.py to run generation-based skip detection via StateDB (instead of being gated on the phantom state.db path).
• Update tests, CLI init gitignore template, and docs to reference state.lmdb/ and the state directory API.

Reviewed changes

Copilot reviewed 42 out of 42 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
packages/pivot/tests/test_skip_detection_integration.py	Update StateDB construction to pass state_dir directly.
packages/pivot/tests/test_run_history.py	Update StateDB construction to use the state directory.
packages/pivot/tests/test_run_cache_lock_update.py	Update test state path to .pivot/ directory instead of .pivot/state.db.
packages/pivot/tests/test_directory_out_integration.py	Clear run cache by removing state.lmdb/ directory rather than phantom files.
packages/pivot/tests/storage/test_state_db_timeout.py	Update timeout tests to pass tmp_path as the state directory.
packages/pivot/tests/storage/test_state.py	Update all state storage tests to use a state directory and state.lmdb/ pathing.
packages/pivot/tests/storage/test_cache.py	Update cache tests to open StateDB with a directory.
packages/pivot/tests/remote/test_transfer.py	Update remote transfer integration tests to construct StateDB(state_dir).
packages/pivot/tests/pipeline/test_pipeline.py	Update wording in docstring to remove state.db reference.
packages/pivot/tests/integration/test_unified_execution.py	Remove get_state_db_path monkeypatch usage.
packages/pivot/tests/integration/test_lazy_resolution.py	Update wording in docstring to remove state.db reference.
packages/pivot/tests/fingerprint/test_no_fingerprint.py	Update StateDB construction to pass state_dir.
packages/pivot/tests/fingerprint/test_fingerprint.py	Switch monkeypatching from get_state_db_path to get_state_dir and update StateDB usage.
packages/pivot/tests/execution/test_executor_worker.py	Update worker/executor tests to construct StateDB from state directory.
packages/pivot/tests/execution/test_executor.py	Update executor integration tests to use .pivot/ as state dir.
packages/pivot/tests/execution/test_execution_modes.py	Update tests that apply deferred writes to use the state directory.
packages/pivot/tests/engine/test_run_history.py	Update state path usage; currently includes redundant get_state_dir monkeypatching.
packages/pivot/tests/engine/test_engine.py	Update engine tests to open StateDB with state_dir.
packages/pivot/tests/conftest.py	Remove get_state_db_path monkeypatch from shared fixture.
packages/pivot/tests/cli/test_fingerprint_cli.py	Update CLI fingerprint tests to use .pivot/ as state dir.
packages/pivot/tests/cli/test_cli_init.py	Remove state.db expectation from .pivot/.gitignore template test.
packages/pivot/tests/cli/test_cli_history.py	Update history tests to open StateDB from .pivot/ directory.
packages/pivot/src/pivot/storage/state.py	Change StateDB.__init__ to accept state_dir and store LMDB under state_dir/state.lmdb.
packages/pivot/src/pivot/status.py	Open StateDB using config.get_state_dir() instead of removed get_state_db_path().
packages/pivot/src/pivot/pipeline/pipeline.py	Update documentation strings to refer to state.lmdb / “state database”.
packages/pivot/src/pivot/fingerprint.py	Replace get_state_db_path() usage with get_state_dir() for StateDB access.
packages/pivot/src/pivot/explain.py	Fix generation-skip detection path by opening StateDB(state_dir, readonly=True) for checks.
packages/pivot/src/pivot/executor/worker.py	Use state_dir from stage_info directly for StateDB open calls.
packages/pivot/src/pivot/executor/core.py	Replace get_state_db_path() usage with get_state_dir() for verification hashing cache.
packages/pivot/src/pivot/executor/commit.py	Construct per-stage StateDB from stage state directory.
packages/pivot/src/pivot/executor/AGENTS.md	Update worker path derivation docs to reflect passing state_dir directly.
packages/pivot/src/pivot/engine/engine.py	Construct cached read-only StateDBs keyed by stage_state_dir rather than state.db path.
packages/pivot/src/pivot/config/io.py	Remove get_state_db_path() accessor.
packages/pivot/src/pivot/config/init.py	Stop exporting removed get_state_db_path.
packages/pivot/src/pivot/cli/remote.py	Open StateDB using config.get_state_dir().
packages/pivot/src/pivot/cli/init.py	Remove state.db from .pivot/.gitignore template; keep state.lmdb/.
packages/pivot/src/pivot/cli/history.py	Open StateDB from config.get_state_dir() (remove state_db_path local var).
packages/pivot/src/pivot/cli/fingerprint.py	Open StateDB from io.get_state_dir() in pivot fingerprint reset.
docs/getting-started/quickstart.md	Update recommended project .gitignore entry to .pivot/state.lmdb/.
docs/concepts/pipelines.md	Update .pivot/ layout docs to show state.lmdb/ directory.
docs/concepts/caching.md	Update caching docs to refer to state.lmdb/.
docs/architecture/overview.md	Update architecture overview to refer to state.lmdb/ directory.

[tbroadley]

@sjawhar Would you mind taking a look at this?