Add reference argument to submodule update --init invocations

[joschock]

When resolving a repo with submodules via the repo_resolver::checkout() method, the reference argument (if appropriate) was not used for submodule updates as part of resolution. This PR adds support for the reference argument to allow references to be used throughout the resolution process.

[codecov]

Codecov Report

Attention: Patch coverage is 66.66667% with 3 lines in your changes missing coverage. Please review.

Project coverage is 78.45%. Comparing base (bf643b0) to head (6f75785).
Report is 74 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #842      +/-   ##
==========================================
- Coverage   78.75%   78.45%   -0.30%     
==========================================
  Files          49       40       -9     
  Lines        4909     4897      -12     
==========================================
- Hits         3866     3842      -24     
- Misses       1043     1055      +12     

Files	Coverage Δ
edk2toolext/environment/repo_resolver.py	91.53% <66.66%> (+1.15%)	⬆️

... and 48 files with indirect coverage changes