This error comes up, if you build your project with Composer and you have added un-registered Git submodules (in file .gitmodules) via a Git commit. A possible solution.
Firstly de-init all Git Submodules:
git submodule deinit --all
Then remove the specific Git submodule "entirely" (uncommited data, commited data and the folder itself):
git rm -rf --cached <path-to-missing-module>
git rm <path-to-missing-module>
Now you can run your packaging/build process with e.g. Composer or Vagrant again. You should get this success message:
Cleared directory 'my/path'
Alternatively you can edit the .gitmodules file to register the Git submodules.