Target --full-rerun to TaxonoPy-specific output files only via manifest

[Copilot]

--full-rerun called shutil.rmtree(output_dir), nuking the entire output directory and any non-TaxonoPy files that happened to live there.

Approach

Rather than pattern-matching filenames (fragile), each run now writes a taxonopy_manifest.json to the output directory recording exactly which files it produced. --full-rerun reads that manifest and removes only those files — nothing else.

Changes

• output_manager.py — two new public functions:
  • write_output_manifest(output_dir, files) — writes taxonopy_manifest.json with paths relative to output_dir
  • read_output_manifest(output_dir) — returns absolute paths from the manifest, or [] if absent/unparseable
• cli.py
  • --full-rerun replaces shutil.rmtree with per-file unlink of manifest entries
  • Both the normal resolve path and the --force-input path call write_output_manifest after output is generated
  • existing_output detection extended to check for manifest presence — more reliable than glob-matching *.resolved.*
• tests/test_output_manager.py (new) — covers manifest write/read, missing/corrupt manifest, and the key invariant that non-TaxonoPy files survive a simulated --full-rerun

Example manifest

{
  "files": [
    "data.resolved.parquet",
    "data.unsolved.parquet",
    "resolution_stats.json"
  ]
}

Original prompt

---

This section details on the original issue you should resolve

<issue_title>Target --full-rerun to TaxonoPy-specific output files only</issue_title>
<issue_description>It is currently too aggressive and may delete unintended data. </issue_description>

Comments on the Issue (you are @copilot in this section)

@hlapp A rogue agent that got implanted into the code? 😉 @thompsonmj Haha, no, just some explosives that could benefit from friendly-fire avoidance ... @thompsonmj To deal with this, options considered include: - Pattern matching to known TaxonoPy output filenames (e.g. `**/*.resolved.*`), but this risks tech debt if naming conventions change and possible collateral damage. Simpler now, but could be improved. - Maintain a record of the exact relevant TaxonoPy output filenames under a directory resulting from a TaxonoPy command. The `--full-rerun` would only act on contents listed in that file for perfect targeting. Having such a manifest would also be a valuable piece of metadata. Better I think.

• Fixes Target --full-rerun to TaxonoPy-specific output files only #28

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[thompsonmj]

Closing in favor of #32