I think you're missing a "git add ." after the symlinking step. Otherwise, I
got a still-empty repo. commit -a only adds already tracked files.
Regardless, I can confirm this behaviour. It does not happen when you do it via
command-line git.
gitg says
** ERROR **: Update index for stage failed
aborting...
upon crashing.
** Changed in: gitg (Ubuntu)
Status: New => Confirmed
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https://bugs.launchpad.net/bugs/598350
Title:
Crash when committing a directory in place of a symlink
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