Application.files refactor

[amandarichardsonn]

This PR adds a operations.py file that holds that holds the functionality that allows user to add files to an Application.

[codecov]

Codecov Report

Attention: Patch coverage is 99.31507% with 1 line in your changes missing coverage. Please review.

Project coverage is 47.32%. Comparing base (cce16e6) to head (6198a14).
Report is 19 commits behind head on smartsim-refactor.

Files with missing lines	Patch %	Lines
smartsim/_core/commands/command_list.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@                  Coverage Diff                  @@
##           smartsim-refactor     #732      +/-   ##
=====================================================
+ Coverage              40.45%   47.32%   +6.87%     
=====================================================
  Files                    110      109       -1     
  Lines                   7326     6573     -753     
=====================================================
+ Hits                    2964     3111     +147     
+ Misses                  4362     3462     -900     

Files with missing lines	Coverage Δ
smartsim/_core/commands/command.py	95.34% <100.00%> (-0.31%)	⬇️
smartsim/_core/generation/generator.py	100.00% <100.00%> (+2.22%)	⬆️
smartsim/_core/generation/operations/operations.py	100.00% <100.00%> (ø)
...rtsim/_core/generation/operations/utils/helpers.py	100.00% <100.00%> (ø)
smartsim/builders/ensemble.py	93.04% <ø> (ø)
smartsim/entity/application.py	90.24% <100.00%> (ø)
smartsim/entity/files.py	52.17% <ø> (-23.10%)	⬇️
smartsim/_core/commands/command_list.py	92.85% <66.66%> (ø)

... and 9 files with indirect coverage changes

[MattToast]

Looks really good! Just dropping some initial feedback so that we can start ironing out some of the finer points, but otherwise this looking really good!

[MattToast]

One last small request, but otherwise LGTM!!