A local text formatting organizer for biomedical/academic writing; use it when you need to clean whitespace/line endings while preserving Markdown structures or when normalizing .docx/.md/.txt before submission or proofreading.
Collapses excessive blank lines while preserving paragraph separation.
Removes trailing spaces at line ends; does not remove leading indentation.
Line ending normalization
Converts all line endings to the selected target (unix/windows/mac).
Indentation normalization
Converts tab characters to spaces when indent=spaces, using indent_size.
Markdown-safe processing
Skips transformations inside fenced code blocks.
Preserves list markers and table pipes/alignment to avoid structural breakage.
DOCX handling
Reads .docx, applies the same normalization at the text/paragraph level, then writes a new .docx using the configured font and size.
When Not to Use
Do not use this skill when the required source data, identifiers, files, or credentials are missing.
Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.
Required Inputs
A clearly specified task goal aligned with the documented scope.
All required files, identifiers, parameters, or environment variables before execution.
Any domain constraints, formatting requirements, and expected output destination if applicable.
Recommended Workflow
Validate the request against the skill boundary and confirm all required inputs are present.
Select the documented execution path and prefer the simplest supported command or procedure.
Produce the expected output using the documented file format, schema, or narrative structure.
Run a final validation pass for completeness, consistency, and safety before returning the result.
Output Contract
Return a structured deliverable that is directly usable without reformatting.
If a file is produced, prefer a deterministic output name such as text_format_organizer_result.md unless the skill documentation defines a better convention.
Include a short validation summary describing what was checked, what assumptions were made, and any remaining limitations.
Validation and Safety Rules
Validate required inputs before execution and stop early when mandatory fields or files are missing.
Do not fabricate measurements, references, findings, or conclusions that are not supported by the provided source material.
Emit a clear warning when credentials, privacy constraints, safety boundaries, or unsupported requests affect the result.
Keep the output safe, reproducible, and within the documented scope at all times.
Failure Handling
If validation fails, explain the exact missing field, file, or parameter and show the minimum fix required.
If an external dependency or script fails, surface the command path, likely cause, and the next recovery step.
If partial output is returned, label it clearly and identify which checks could not be completed.
Quick Validation
Run this minimal verification path before full execution when possible:
python scripts/init_run.py --help
Expected output format:
Result file: text_format_organizer_result.md
Validation summary: PASS/FAIL with brief notes
Assumptions: explicit list if any
Deterministic Output Rules
Use the same section order for every supported request of this skill.
Keep output field names stable and do not rename documented keys across examples.
If a value is unavailable, emit an explicit placeholder instead of omitting the field.
Completion Checklist
Confirm all required inputs were present and valid.
Confirm the supported execution path completed without unresolved errors.
Confirm the final deliverable matches the documented format exactly.
Confirm assumptions, limitations, and warnings are surfaced explicitly.