You could alter the make file (if you are using it) portion that does the zipping, or exclude it manually if manually zipping. We just use a repo with a structure that can contain more than one channel, and the .git dir isn't at any part where it would be zipped with a channel.
E.g.
REPO_ROOT
.git/
source/
test_channel/
manifest
images/
source/
other_channel/
manifest
images/
source/
zips/
In fact, copying the layout of the SDK to some degree may work well, that's what we did.
-- GandK Labs
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