Git checkout/pull doesn't remove directories?

Git doesn't track directories, so it won't remove ones that become empty as a result of a merge or other change. However, you can use git clean -fd to remove untracked directories (the -fd flag means force removal of untracked files and directories).

I had same issue, in my case on build service (CI).. as GIT pulls all files without cleaning folders, all the bin / obj that were previously builded by the CI are dirty, so If I remove a test project, the bin will still contain the DLL and will mention tests that does not exist.

In order to solve this issue; this command seems to do the trick (at least for me)

git clean -fd -x

where X will remove all untracked files:

-X Remove only files ignored by Git. This may be useful to rebuild everything from scratch, but keep manually created files.