On 2014-03-21 17.13, Matthias Beyer wrote:
> Hi,
> I struggled with a really nasty issue today (and yesterday):
> I work on a semester project paper which is written in latex and
> therefor version-controlled with git. We compile the document using
> pdflatex, we automate the compiling with make.
> pdflatex generates some temporary files, which are required if you
> call it the second and third time (it is a top-down compiler, which
> needs to be called several times). One of the file extensions is
> ".idx", which (kind of) conflicts with file extensions in .git/.
> Unfortunetely, we wrote our `make clean` task recursively. I think you
> can imagine what went wrong: The clean-task corrupted the repository,
> as it removed .idx files from within .git/.
> I lost work because of this ugly name collision.
> My question now:
> I know, I can fix this by fixing the clean task in my Makefile. But
> maybe someone somewhere on this world doesn't know the git internals
> as good as me (and, of course, my coworker). Is there _any chance
> at all_ that this gets mentioned somewhere, so others don't fall into
> this pit?
The idx files are mentioned here:

(Otherwise, some random thoughts:)
- stay out of the .git directory, whatever you do
   (I lost some data because my faulty scripts using sed to replace
   "s/this/that/" and went into the .git directory) 
- Don't delete "read-only" files
   (The .idx files are all  "r--r--r--")
  Or in other words, do not use "rf -f" in a script, unless you know exactly
  what you and the script are doing.
- Replace "rm -f" whith "mv /tmp" could be an option
- As mentioned before, "git clean" can be an option,
  I used it once when the "make clean", "make distclean", "make reallydistclean"
  did not work as expected by me,
  some auto-generated config files where still not deleted. 
- Make backups of your repo (frequently)
- push the repo to a backup repo (frequently)
- Use $GIT_DIR to move the repo out of your work tree:

- Prepare a patch that renames the *.idx files used by Git into
  *.gitidx, *.gidx, *.packidx, (and the *.pack into *.packdata ??) 

Hopefully you did not loose too much data, and if you have an idea how to 
things, you may consider sending a patch, improvements are possible and welcome.

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