Follow this workflow end-to-end unless the user explicitly asks to skip steps
1) Intake and scope
- Confirm input artifacts: TeX source path(s), PDF path, supplementary files, target repository, and expected outputs.
- State assumptions explicitly when information is missing.
- Keep approach adaptable to the specific paper; do not force a fixed dependency stack or rigid project template.
- Check whether the working folder already contains paper source files (
.tex,.bib, style files, f
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