Is there a possibility to nicely version and track git hooks? Can I safely have another (nested) git repository under the hook folder on server?
Nothing prevents you to add your gitolite server hooks to a admin repo (or even the gitolite admin repo, where you are adding public ssh keys and the config file for all the repos and associated rights).
However pushing that admin repo back to the gitolite server won't trigger anything hook-wise.
You will still have to go to the hook folder on the server and:
It seems clearer to have a dedicated repo for server hooks (itself declared in Gitolite), instead of burying a Git repo within a technical folder of Gitolite.
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