Untracked files after switching from submodule to directory

[agners]

On a self-hosted runner, using actions/checkout@v2 on a repository which uses a submodule in directory x/, subsequently doesn't remove that submodule when it gets converted to a directory.

1. Create repository with submodule in directory x/
2. Use GitHub actions with actions/checkout@v2, observe that the main repository and directory x/ is correctly checked out
3. Remove submodule x/ from repository, converting it to a regular "native" directory commited to the main repository
4. Use GitHub actions with actions/checkout@v2. Directory x/ still contains the submodule. git seems not to cleanup/checkout the root repository folder x/. The directory contains untracked files.

The clean property is left default (which is true). It seems that git commands are not able to cleanup existing submodules in the working directory when moving from a branch with submodules to a branch without submodules.

It seems that the .git file of the submodules make git to stop recursing into those directories and not checking them out. Removing .git files of those removed submodules seems to help:

find ./ -name .git -type f -exec rm {} \;

This is particular annoying when moving from submodules to directory back and forth, e.g. when using the same runners for a stable branch and development branch.

[agners]

The work around removing the .git file only works when moving from git repo with submodule -> git repo without submodule. When a git repository with submodule is used, removing the .git file causes the submodule loosing track of what files belonging to the submodule. When the submodule is updated, all files which have been removed in that submodule will stay in the submodule directory (which can be problematic of course!).