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Directory and Files For Your Paper

1. [Assigned Number] If you are the first or writing author of a paper where I will be a co-author, please send me a description of the paper (ideally title and abstract), and I will send you an assigned number. [NOTE 1.1: All examples below use the number 58 for illustration purposes. DO NOT use 58, but your assigned number instead.] [NOTE 1.2: The $ sign marks example commands to be executed in a shell.]
2. [Directory] Create a directory named paper followed by your assigned number. [Example: $ mkdir paper58]
3. [GIT] Initialize git repository in that directory. [Example: $ cd paper58; git init]
4. [README] Create a plain text README file with a description of this paper, ideally title and abstract. git add this README file.
5. [Manuscript] Create a draft/v1 directory containing your first version of your paper. git add your manuscript file.
6. [Figures] Inside draft/v1 git add PDF figures to be included. It is best if you include in this directory and git add the tikz or gnuplot sources for the figures, and all dependent data files.
7. [Bibliography] Use thesis.bib by linking it, do not copy thesis.bib, do not git add thesis.bib. git add the produced bbl file. Do not submit thesis.bib to journal, submit generated bbl file instead. [Example: $ ln -s ../../../thesis/thesis.bib; pdftex paper58; bibtex paper58; git add paper58.bbl]
8. [Compilation] Add all files required for TeX compilation of your manuscript. DO NOT git add files produced by TeX except for the bbl file.
9. [Supplemental] Include supplemental in draft/v1 with all auxiliary files needed to compile the TeX. Guidelines to write such supplemental will be provided in a different memorandum.
10. [Letter] Letter to the editor should be in plain text, and git added under draft/v1
11. [Results] The directory results may optionally be present, and used to store cooked results, but don't git add big files.
12. [Papers] The directory papers may store PDFs of relevant papers. Do NOT git add them.
13. [Discussions] The directory theory may contain text files of discussion that won't appear in paper or supplement. Add here emails and discussion related to the paper. This may be committed to git.
14. [Versions] draft/v2 may optionally contain the new version of the paper after referees comments, git add answer to referees in this directory as well. Additional optional directories, such as draft/v3, can be added only if there are subsequent resubmissions until publication. Source files in all these directories should be added.
15. [arXiv] The directory arXiv/v1 should contain the version submitted to the arXiv. If other versions are posted in the arXiv they may be located in directories arXiv/v2, etc. git commit all source files.
16. [Business Sensitive] The whole directory must be treated as Business Sensitive and NOT publicly posted. This remains true even after publication.
17. [Data preservation] All published raw data must be preserved and archived long term.

Example of directory structure

directory		Description
paper58/
paper58/.git		Git directory, created automatically by git init
paper58/README		Contains description of this paper, ideally title and abstract
paper58/draft/v1		First version of the draft, including first submission Directory contains cooked figures, and supplemental, and all files needed to compile TeX sources. Link thesis.bib here as well. Include and git add letter to the editor in this directory. Git commit all sources files. DO NOT git add files produced by TeX, except for the bbl that must be submitted. DO NOT git add thesis.bib, just link it. Git add the figures in PDF. It is best if you include in this directory and git add the tikz or gnuplot sources for the figures, and all dependent data files.
paper58/draft/v2		[optional] Resubmission, after referees comments, include answer to referees in this directory.
paper58/draft/v3		[optional] Add a version only if there is another resubmission
...
paper58/arXiv/v1		contains the first version submitted to the arXiv. git commit all source files.
paper58/arXiv/v2		[optional] If other versions are posted in the arXiv they may be located in directories arXiv/v2, etc. git commit all source files.
...
paper58/results		[optional] Cooked results, don't add big files here
paper58/papers		[optional] You may store here PDFs of relevant papers. Do NOT git add them.
paper58/theory		[optional] Add here .tex files containing discussion that won't appear in paper or supplement. Add here emails and discussion related to the paper. This may be committed to git.