Git submodules in Source not fully supported

[hagertnl]

The way Git initializes submodules, the .git sub-directory within the Git repo that's a submodule is actually a file that points to APPROOT/.git/modules/path/to/submodule.

For example, a Git submodule inside a test's Source directory:

$ pwd
/.../APPROOT/qmcpack_amd_compiler_bug_hpecoe94/Source/qmcpack

$ cat .git
gitdir: ../../../.git/modules/qmcpack_amd_compiler_bug_hpecoe94/Source/qmcpack

So, once this is copied to build_directory, that relative path is broken.

I'm not sure how we should deal with that, but the first option that comes to mind is having the harness understand the structure of APPROOT/.git/modules, and be able to automatically replace the .git files with the .git subdirectory from APPROOT/.git/modules. It's fairly trivial to look at the directories in APPROOT/.git/modules and see if that applies to the Source directories you just copied.