Remove dependence on parmed

[SimonBoothroyd]

Description

This PR aims to completely strip the dependance of femto on parmed. It hasn't really been in active development for a long while now, and it is limiting in terms of what force fields can be used with the package. Things like virtual sites or class II FF terms, for example, would not be supported when using ParmEd.

Further, this PR adds support for co-factors to all APIs. This PR does not handle updating the directory structure, or CLIs, as this will be handled in a future PR.

TODO:

• Re-add support for .parm7 files.
• Test SepTop impl.
• Test ATM impl.

Status

• Ready to go

[codecov]

Codecov Report

Attention: Patch coverage is 95.89041% with 15 lines in your changes missing coverage. Please review.

Project coverage is 95.59%. Comparing base (4023514) to head (3715ff8).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
femto/md/utils/amber.py	92.40%	6 Missing ⚠️
femto/fe/atm/_setup.py	90.90%	3 Missing ⚠️
femto/fe/septop/_setup.py	93.18%	3 Missing ⚠️
femto/md/prepare.py	98.31%	2 Missing ⚠️
femto/fe/reference.py	96.87%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #27      +/-   ##
==========================================
- Coverage   95.62%   95.59%   -0.04%     
==========================================
  Files          46       45       -1     
  Lines        3039     3084      +45     
==========================================
+ Hits         2906     2948      +42     
- Misses        133      136       +3     

Flag	Coverage Δ
unittests	95.59% <95.89%> (-0.04%)	⬇️

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