I know that having an exclude option for notmuch has been discussed a
number of times. I have wanted such a feature to be able to ignore the
.git directroy, since I keep my mail in a git repository. I recently
discovered a workaround.

If you make .git a text file containing
===== .git ====
gitdir: .notmuch/git
===============
and move the .git directory to .notmuch/git, git will behave as if it is
a normal repository, and notmuch will ignore .notmuch/git. notmuch will
warn once about .git not being a mail file, but since it is static, it
won't warn about it every time one does 'notmuch new'.

  Tom