chore: trim dead code, modularize CLI, and archive stale docs
Extract review-plan, report, quarantine, state, and config handlers into commands/ with shared cli_helpers; remove unused exceptions and duplicate plan summary wrappers. Archive superseded review markdown, sync docs to 517-test baseline, and fix empty series titles when only a quality tag remains. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com> Co-authored-by: Cursor <cursoragent@cursor.com>
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Claude Sonnet 4.5
Cursor
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## Project Structure & Module Organization
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- Core package lives in `src/vlm/`.
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- CLI entrypoint is `src/vlm/cli.py` (`vlm` console script). Commands use `pass_context` and `CLIContext` from `context.py`; command logic is modularized in `commands/` (e.g. `scan`, `parse`, `enrich`, `analyze`, `plan`, `execute`).
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- CLI entrypoint is `src/vlm/cli.py` (`vlm` console script). Shared CLI helpers live in `cli_helpers.py`. Command logic is in `commands/` (scan, parse, enrich, analyze, plan, execute, review_plan, report, quarantine_cmd, state_cmd, config_cmd).
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- Functional modules by concern: scanning (`scanner.py`), parsing (`parser.py`), enrichment (`enrichment.py`, `cache.py`, `providers/`), analysis/planning/execution (`analysis.py`, `planner.py`, `executor.py`), I/O helpers (`io.py`), utilities (`utils.py`), state/reporting/logging (`state.py`, `reports.py`, `logging_config.py`), config (`config.py`), models (`models.py`).
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- Tests live in `tests/` and mirror feature areas (e.g. `tests/test_scanner.py`, `tests/test_cli_state.py`, `tests/test_enrichment.py`).
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- Project metadata and tool config are in `pyproject.toml`.
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