v0.4.0

What's Changed

• feat: add multi-root watch support by @Mathews-Tom in #45

Full Changelog: v0.3.0...v0.4.0

codevigil 0.3.0

This release graduates codevigil from a live-only watch dashboard to a persistent-memory tool with cold-ingest, cohort trend analysis at parity with anthropics/claude-code#42796, and a project-level watch roll-up. The 0.2.x watch command is preserved behind --by-session; the new default collapses multi-session projects into a single row.

Added

• Persistent processed-session store (SQLite) (analysis/processed_store.py). codevigil watch now writes a durable record for every finalised session under ~/.local/state/codevigil/processed/ — session id, file id, cursor offset, collector state snapshot, and derived metric summary. The watcher seeds each polled file from the stored cursor so restarts no longer re-parse JSONL from byte 0. The collector state is restored verbatim so rolling windows survive across process restarts. See docs/design.md §Persistent Memory for schema, migration policy, and the key invariants the store upholds.
• codevigil ingest subcommand. One-shot cold-ingest of every JSONL session under watch.root into the persistent store. Intended to be run once after install (or once after any --force rebuild) so subsequent codevigil watch ticks only process newly-appended events. Flags: --db PATH (override the store path) and --force (re-ingest every session, ignoring existing rows). Missing-store bootstrap is automatic: codevigil watch will invoke the ingest flow on first run if the store is absent.
• Per-file cursor cache (watcher_cache.py). Opt-in-by-default persistent cache under ~/.local/state/codevigil/ that records (inode, mtime, size, byte_offset) per watched file. The watcher consults the cache on startup and seeks past already-processed bytes. Disable with watch.cursor_cache_enabled = false for fully reproducible cold-start benchmarks. Cache location is configurable via watch.cursor_cache_dir.
• Project-row watch view (renderers/terminal.py). The default codevigil watch layout now rolls up every active session belonging to the same project into a single row showing the fleet-worst severity, the active session count, and the aggregate metric summary. The previous one-block-per-session layout is available via the new --by-session CLI flag or by setting watch.display_mode = "session" in config. watch.display_project_limit (default 10) caps the number of project rows rendered per frame and is analogous to watch.display_limit for session mode.
• thinking collector (collectors/thinking.py). Observes EventKind.THINKING events and exposes the visible-vs-redacted ratio plus median visible-block and signature-block character lengths. Headline signal for the #42796 "thinking depth decline" cohort analysis. Severity is always OK by design — the collector is descriptive, not a quality gate.
• prompts collector (collectors/prompts.py). Counts user-message turns per session. Primary scalar feeds the #42796 "prompts per session" per-week cohort mean. Severity is always OK.
• Both new collectors are enabled by default. collectors.enabled now ships as ["read_edit_ratio", "stop_phrase", "reasoning_loop", "thinking", "prompts"] so cohort reports surface the #42796 signals out of the box. Each has its own [collectors.thinking] / [collectors.prompts] config section with an experimental flag.
• codevigil report --pivot-date YYYY-MM-DD splits the corpus into before / after buckets (after-bucket inclusive) and emits a Before/After delta table. Incompatible with --group-by and --compare-periods.
• codevigil report --experimental-correlations appends a Pearson correlation matrix across per-session metrics to the cohort report. Pairs below MIN_PAIRS=30 are dropped; zero-variance columns are skipped. Surfaces with an unavoidable "exploratory signal, not causal evidence" disclaimer and is marked [experimental] in output.
• codevigil report --output-file PATH writes the rendered report to an exact file path instead of the computed <output_dir>/report*.{json,md,txt} default. Parent directories are created if missing; the path must resolve under $HOME. Mutually exclusive with --output.
• codevigil report --format csv on the cohort path. Emits a flat dimension_value,metric_name,mean,stdev,n,min,max schema for notebook consumption. Per-session JSON / Markdown remain unchanged.
• Cohort report methodology header on every --group-by report. Shows corpus size, date range, cell count, and the cohort JSON schema version so readers know the data shape before reading the table.
• Δ-vs-prior-row annotations on chronological dimensions (day, week) for each cell with n≥5, plus threshold highlighting that renders cells crossing the warn / critical thresholds in bold (critical cells carry a leading asterisk). Direction is per-metric (parse_health low-is-bad; reasoning_loop / stop_phrase high-is-bad).
• Cohort column injectors expose four new metric columns: blind_edit_rate, research_mutation_ratio, thinking_visible_ratio (+ two chars_median companions), and user_turns. Column headers are decoupled from collector internals so naming stays self-explanatory.
• Claim-discipline renderer gate (tests/report/test_claim_discipline.py). Every public cohort renderer is walked and any output containing banned causal language (because of, due to, results in, responsible for, etc.) fails the build. Correlation-not-causation enforced at test time.

Changed

• Default watch layout is now the project roll-up. codevigil watch with no flags renders one row per project; pass --by-session for the 0.2.x-style per-session blocks. Scripts screen-scraping the watch output must either pin --by-session or migrate to the new layout.
• collectors.enabled default now includes thinking and prompts. Users with an explicit collectors.enabled in their config file are unaffected — their override wins. Users relying on the default will see two new collector blocks in watch output and two new metric columns in cohort reports after upgrading.

Fixed

• Stale cursor seeds on file replacement (watcher.py, watcher_cache.py). When a session JSONL was replaced in place (e.g., by Claude Code compaction writing a new file with the same path but a different inode / smaller size), the cursor cache previously seeded the new file from the old byte offset, silently skipping the early events. The cache loader now refuses any seed whose (inode, size) fingerprint does not match the current file on disk and falls back to byte 0 with a single-line WARN naming the replaced path. A regression test at tests/test_watcher_cursor_cache.py covers the inode-change and shrink-below-offset cases.

Developer experience

• Large-scale complexity reduction across cli.py, config.py, parser.py, report/, history/, analysis/, collectors/, and renderers/. No behavioural change — pure extraction of helpers, defaultdict adoption, nesting flattening. mypy --strict still clean; every pre-existing test passes unchanged.
• New integration and unit tests: tests/test_cli_ingest.py, tests/test_processed_session_store.py, tests/test_watcher_cursor_cache.py, tests/test_watch_resume_collector_state.py, tests/test_watcher_timing_instrumentation.py, tests/test_watcher_unresolved_timestamp.py, tests/test_collector_state_serialization.py, tests/test_parser_structural_kinds.py, tests/renderers/test_terminal_project_view.py, tests/renderers/test_terminal_store_overlay.py, tests/cli/test_report_output_file.py, tests/cli/test_watch_instant_shutdown.py.