Commiting automatically (2)

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Some time ago I asked how to make a commit of the working tree in a way 
influencing neither the current branch nor the index:
http://comments.gmane.org/gmane.comp.version-control.git/157056
I'm going to use it for taking a snapshot of the current working tree without 
disturbing my work. It seem to work except for one thing:

There are files tracked by git and later added to .gitignore. AFAIK listing 
them in .gitignore is a no-op, since I haven't removed them from the index. 
Until now I haven't known about them at all, I'm currently undecided what to do 
to them.

However, when I use my git-autocom script, those files get marked as deleted. 
This is quite strange, especially because of them still existing. I'd strongly 
prefer git-autocom to behave just like git commit (i.e., tracking the files).

The relevant part of my script follows:

export GIT_INDEX_FILE=.git/autocom.tmp
git add -A &&
tree=$(git write-tree) &&
commit=$(echo "$message" | git commit-tree $tree $parent1 $parent2) &&
git update-ref -m "$message" refs/heads/autocom $commit

I'd say using another index is the reason for this behavior. The index gets 
created on the first use, which is probably why those files look like being 
deleted. Should I always
/bin/cp .git/index $GIT_INDEX_FILE
or is there a better way?

There's one more problem. My script doesn't recognize deleted files, since
git add -A
does nothing to them. I'm quite sure I saw a solution to this, but can't find 
it now...

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