documentation-writer

name: documentation-writer description: Create or update user-facing technical documentation (mzmine module docs / wiki pages) from implementation code and existing docs. Follows the project documentation template, fact-checks claims against code, preserves legacy pages, and updates navigation. TRIGGER when the user says "update/edit/write/fix/improve the docs/documentation/wiki/module page" for any module, parameter, or feature; when adding screenshots or sections to an existing .md page under mzmine_documentation/docs/; when asked to document a new module, parameter, or algorithm; or when migrating/reconciling docs with current code. SKIP for inline code comments, Javadoc, README files in source repos, commit messages, PR descriptions, or generated API docs.

Documentation Writer

Core workflow

1. Define scope and constraints.

• Extract the requested target location, audience, template/style requirements, and explicit do-not-touch files.
• Convert user instructions into an acceptance checklist before writing.

2. Gather authoritative sources.

• Read the documentation template/style guide first: ..\mzmine_documentation\docs\contribute_docu_template.md
• Read current implementation code and parameters before drafting behavior claims.
• Read legacy docs only as examples or migration context. They are at ../mzmine_documentation

3. Build a fact map from code.

• List each user-facing claim you plan to document (inputs, outputs, defaults, formulas, errors, side effects).
• Attach each claim to a concrete source location (file and line).
• Mark uncertain claims and resolve them before writing.

4. Draft the new documentation page.

• Follow the required template sections and heading structure.
• Prefer concise, user-facing wording; include formulas and decision rules only where they change outcomes.
• Add warnings/tips for failure modes, prerequisites, and edge cases.
• Keep content general enough for long-term maintenance; avoid one-off troubleshooting details unless requested.
• When adding scientific citations, make sure they are specific to the documented module and not a general resource

5. Integrate into navigation when needed.

• If the request is for user-facing wiki docs, add/update navigation entries so the page is discoverable.
• Do not modify unrelated or protected legacy pages unless explicitly requested.

6. Validate and sanity-check.

• Re-read the final markdown for consistency with the fact map.
• Run docs build/lint if available; if unavailable, report that clearly.
• Check for broken relative links and missing assets referenced by the page.

7. Report results and mismatches.

• Summarize what was created/updated.
• Explicitly report inconsistencies found between legacy docs and current implementation.
• Distinguish confirmed facts from inferred behavior.

Writing standards

• Use implementation-truth over historical wording.
• Keep parameter descriptions action-oriented: what it controls, valid options, defaults, and practical impact.
• Document output artifacts (new columns, stored metadata, generated files, or persisted parameters).
• Call out behavior that may surprise users (legacy scaling, interpolation rules, fallback logic, hidden persistence).
• Avoid copying outdated statements from older docs without verification.

Output checklist

Before finishing, confirm:

• Target markdown file was created in the requested location.
• Template/style requirements were followed.
• Legacy files were left unchanged if requested.
• New page is linked in docs navigation when applicable.
• Fact-check findings were reported with concrete references.