Scaffold a new paper repository

Scaffold a new paper repository

Bootstrap a new LaTeX paper repo with the recommended layout (see /paper:explain). Output: a <path>/ directory that compiles cleanly to paper.pdf from minute zero, with all the build infrastructure in place so the user can immediately start writing.

Arguments in $ARGUMENTS:

• $0 — target directory (e.g. ~/GitHub/my-new-paper). Created if missing.
• --journal=mnras|aa|apj — journal style (default mnras).
• --title="..." — paper title (defaults to placeholder).
• --author="..." — first-author name (defaults to \\author{TBD}).

Steps

1. Create the directory + initialise git if not already. Create subdirs: figures/, scripts/.

2. Fetch the journal class file + bibstyle. From CTAN mirrors:

   # mnras
   curl -sSL -o mnras.cls "https://mirrors.ctan.org/macros/latex/contrib/mnras/mnras.cls"
   curl -sSL -o mnras.bst "https://mirrors.ctan.org/macros/latex/contrib/mnras/mnras.bst"
   # aa
   curl -sSL -o aa.cls    "https://mirrors.ctan.org/macros/latex/contrib/aa/aa.cls"
   curl -sSL -o aa.bst    "https://mirrors.ctan.org/macros/latex/contrib/aa/aa.bst"
   

   For ApJ / AAS, ask the user to manually download aastex631.cls from https://journals.aas.org/aastexguide/.

3. Write paper.tex from the journal-specific skeleton in /paper:explain (look there for the exact preamble). Default sections: Abstract (no citations), Introduction, Methods, Results, Discussion, Acknowledgements, Data Availability, Bibliography. Include the TikZ preamble even if not used yet.

4. Write references.bib — empty placeholder with a header comment.

5. Write Makefile with targets all, figs, clean, distclean, help (see /paper:explain for the template).

6. Write .gitignore with the standard LaTeX + Python ignore pattern.

7. Write LICENSE (default MIT, ask the user if they prefer otherwise).

8. Write README.md with build instructions (make figs, make, dependencies).

9. Generate placeholder figures so latex compiles. For each \includegraphics in the skeleton, emit a 6x4 PNG with the filename as the placeholder text. Use the recipe in /paper:explain.

10. Verify with latexmk -pdf -interaction=nonstopmode paper.tex. Expect zero errors, undefined-reference warnings (because references.bib is empty) are OK.

11. Report back:

    • Files written (absolute paths)
    • paper.pdf page count + size
    • Suggested next steps:
      • /paper:refs <topic1> <topic2> ... to populate bibtex
      • Edit paper.tex to fill in content
      • /paper:build for incremental rebuilds

Pitfalls

• CTAN mirror selection: if mirrors.ctan.org times out, fall back to a specific mirror like mirror.ctan.org or texlive.info. The mnras.cls is in texlive so any TeX Live install also has it (kpsewhich mnras.cls) — vendoring is for reproducibility.
• Existing directory: if <path> already has a paper.tex, STOP and ask the user before overwriting.
• Journal class options matter: MNRAS wants [a4paper, fleqn, usenatbib]; the class compiles but renders weirdly without usenatbib.