Replace TaggedFilesHierarchy with os.walk and implement configure_directory entrypoint

[amandarichardsonn]

This PR adds a configure_directory entry point, as well as tests. It also removes TaggedFilesHierarchy and replaces it with os.walk. Finally, the Generator tests have been refactored.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 46.24%. Comparing base (cce16e6) to head (dfbb53f).
Report is 16 commits behind head on smartsim-refactor.

Additional details and impacted files

@@                  Coverage Diff                  @@
##           smartsim-refactor     #695      +/-   ##
=====================================================
+ Coverage              40.45%   46.24%   +5.78%     
=====================================================
  Files                    110      107       -3     
  Lines                   7326     6446     -880     
=====================================================
+ Hits                    2964     2981      +17     
+ Misses                  4362     3465     -897     

Files with missing lines	Coverage Δ
smartsim/_core/commands/command_list.py	97.61% <100.00%> (ø)
smartsim/_core/generation/generator.py	100.00% <100.00%> (+2.22%)	⬆️
smartsim/entity/__init__.py	100.00% <ø> (ø)
smartsim/entity/files.py	71.73% <ø> (-3.53%)	⬇️
smartsim/experiment.py	86.52% <100.00%> (+4.97%)	⬆️

... and 8 files with indirect coverage changes

[juliaputko]

1 minor comment, otherwise lgtm!!

[MattToast]

Just some initial feedback while the CI gets worked out. So far looks good!

[mellis13]

Just some general comments to get the review process started.

[mellis13]

Just a couple of comments/questions.

[mellis13]

Only one small item but otherwise I think this is ready to merge and other items can be addressed as the user API for attaching files is updating. Thanks!