Additions/deletions of an externals submodules can lead to a modified status after running checkout_externals

[billsacks]

Summary of Issue:

In some situations, changing the version of an external that has submodules and then running checkout_externals can result in that external having a modified (M) status. This prevents subsequent runs of checkout_externals unless you remove the offending external or do something to bring it back into sync. I can't tell whether the offending external is actually in a modified state or if manage_externals just thinks it is.

For the reproducer below (changing between ctsm5.1.dev029 and ctsm5.1.dev030), @gold2718 's hypothesis about the cause is:

The CDEPS hash in 029 has one submodule, fox.
The CDEPS hash in 030 has two submodules, fox and genf90

When you checkout the externals in 029, manage_externals initializes the submodules in CDEPS.
When you checkout the externals in 030, manage_externals does NOT initialize the submodules in CDEPS because it thinks they are already initialized. This leaves genf90 (the new submodule) as not initialized.

I believe that if you tried this sequence where new submodules are not introduced, there will not be a problem.

To avoid removing cdeps, you can:
cd cdeps
git submodule init
git submodule update
cd ..

For what it's worth, I think I have also run into this problem going the other way (from dev030 to dev029, resulting in a deletion of one of CDEPS's externals).

Expected behavior and actual behavior:

Expected behavior: after running checkout_externals, no externals should be in a modified state.

Actual behavior: in some situations, after running checkout_externals, externals with submodules can be in a modified state.

Steps to reproduce the problem (should include model description file(s) or link to public repository):

git clone [email protected]:ESCOMP/CTSM.git
cd CTSM
git checkout ctsm5.1.dev029
./manage_externals/checkout_externals cdeps
git checkout ctsm5.1.dev030
./manage_externals/checkout_externals cdeps
./manage_externals/checkout_externals -S cdeps

gives:

 M  ./components/cdeps
    ./components/cdeps/fox
    ./components/cdeps/share/genf90

What is the changeset ID of the code, and the machine you are using:

The above CTSM version is using manage_externals at 39ad532.

have you modified the code? If so, it must be committed and available for testing:

No

Screen output or log file showing the error message and context:

See above reproducer