Remove freephil dependency and refactor command line

[noemifrisina]

Closes #349

Also fixes #221 by tidying up the tests

[codecov]

Codecov Report

Attention: Patch coverage is 37.89062% with 159 lines in your changes missing coverage. Please review.

Project coverage is 46.37%. Comparing base (0e3eecb) to head (d0e7396).
Report is 14 commits behind head on main.

Files with missing lines	Patch %	Lines
src/nexgen/command_line/nexus_generator.py	0.00%	113 Missing ⚠️
src/nexgen/command_line/parse_utils.py	50.00%	17 Missing ⚠️
src/nexgen/command_line/ED_nexus.py	0.00%	13 Missing ⚠️
src/nexgen/command_line/cli_config.py	87.87%	4 Missing and 4 partials ⚠️
src/nexgen/beamlines/beamline_utils.py	0.00%	5 Missing ⚠️
src/nexgen/command_line/SSX_cli.py	0.00%	2 Missing ⚠️
src/nexgen/nxs_write/ed_nxmx_writer.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #351      +/-   ##
==========================================
+ Coverage   40.65%   46.37%   +5.71%     
==========================================
  Files          49       46       -3     
  Lines        4287     3987     -300     
  Branches      592      527      -65     
==========================================
+ Hits         1743     1849     +106     
+ Misses       2432     2019     -413     
- Partials      112      119       +7     

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