• cryptobib bibliography
• cryptocode macros
• \anonynmous{foo}{bar} to hide/show information during submission/after
• \tikzexternalizemaybe to enable tikzexternalize depending on value of buildexternal
• ~.dir-locals.el~ according to my taste
• ~.projectile~ according to my taste
• Extensive .gitignore

• The paper is in paper.
• Code goes into code.
• Data goes into data.
• Cryptobib is in a directory pointed to by BIBINPUTS=.:/path-to/cryptobib
• Scripts write to paper/constants.tex for use with pgfkeys.

If you want to do local modification to .dir-locals.el which is under version control, you can use

git update-index --assume-unchanged .dir-locals.el

to tell git to ignore changes to that file. Use

git update-index --no-assume-unchanged .dir-locals.el

to undo.