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[jgit-dev] Clones of JGit bare repos act strange

Hello,

I'm using JGit to create and initialize bare repositories and noticed
that clones thereof (using vanilla git) act a little bit strange.
Doing something like "git reset --hard" will toggle repeatedly between
all files getting staged for deletion and the default (expected)
"nothing to commit (working directory clean)" state.

Here is a short standalone example: https://gist.github.com/3298119

Am I missing something?

Thanks,
 Roger