Fixes _find_gitroot for E3SM provenance

[jasonb5]

The function _find_gitroot would error when trying to determine the
models .git directory when being used as a submodule of another
project.

The error would occur when trying to copy a git metadata
file for provenance whose path was relative to the git repository.

This required two fixes, the first was to resolve the relative path and
the second was handling a third scenario for determining the model's
.git directory.

Test suite: scripts_regression_tests
Test baseline: n/a
Test namelist changes: n/a
Test status: n/a

Fixes #4251
User interface changes?: n
Update gh-pages html (Y/N)?: n