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Re-set Kohana submodule
My fix is to do the following:
$: rm -rf core/kohana
$: vim .gitmodules
Delete the submodule path to kohana from this file.
$: git rm --cached core/kohana
$: git submodule add git@github.com:crowdfavorite/kohana.git core/kohana
$: git submodule init --recursive
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