Timothy Kassis 3378ecea57 citation-management: correct documented commands, bump to 2.0 ...

SKILL.md's one copy-pasteable Phase 3 command used --remove-duplicates, which
argparse rejects; the real flag is --deduplicate. A sweep of every documented
invocation against the actual --help output found eleven more flags that do not
exist: validate_citations.py --auto-fix, --strict, --output,
--check-required-fields, --check-authors, --check-duplicates, --check-syntax;
format_bibtex.py --validate, --report, --style; doi_to_bibtex.py --clipboard;
and search_google_scholar.py --open-access-only. Several sat in worked examples
an agent would run verbatim.

citation_validation.md documented an "auto-fix" mode of validate_citations.py
that never existed -- the script only reports. Those sections now point at
format_bibtex.py, which is what rewrites.

Other corrections:

- --report wrote a JSON document to report.txt.
- three of five declared dependencies were never imported.
- Phase 2.5 was marked MANDATORY but needed web access that allowed-tools did
  not grant; WebSearch and WebFetch are now declared.
- no compatibility field, despite needing a Python version, a package, and
  network access.
- the schematics section told a citation skill to produce diagrams by default,
  and named generate_schematic.py while generate_schematic_ai.py sat beside it
  unexplained. Reduced to a pointer at scientific-schematics.
- venue reference counts are labelled as rules of thumb rather than submission
  requirements, which is what they are.

Documents search_openalex.py and the shared _common.py, and regenerates the
workflow diagram, which no longer matched what the skill does.

Version 1.8 -> 2.0: format_bibtex.py no longer overwrites its input by default.

2026-07-31 10:59:16 -07:00

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