[Backport] Do not apply patches if sub non-git repo is located in a git repo. #540
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[Backport] Do not apply patches if repo is a not a git repo. #539
[Backport] Do not apply patches if sub non-git repo is located in a git repo. #545
Also add an option to control patch apply which is default on. Pass -DAPPLY_PATCHES=OFF will skip patch apply process.