mkdocs build --clean wipes out the project when attempting to split doc development and mkdocs' build output across two git branches (gh-pages, gh-pages-dev) with the following layout:

<branch: gh-pages-dev>
$PROJ_ROOT/
|- dev
`  |- doc/
   `- mkdoc.yml  \# NOTE: site_dir=../

<branch: gh-pages>
$PROJ_ROOT/
`- ... \# build output

This is so I can both keep everything in the same project and also track the dev/ directory on the dev branch and have the output where it should be on the gh-pages branch. It seems obvious now that this would wipe out everything including the .git/ for the project (glad this was a test). Possibly, it could recursively check site_dir for a .git, warn and exit. Or just a disclaimer here of this possibility would be enough, so no one else tries this and wipes out their project (and maybe you could recommend to new users how to maintain site development and build output in the same repo).

Thanks,
Kris