Cleanup settings structure

[BwKodex]

Cleans up settings management and classes.

In addition, a setting for adding an output directory for where to save the plot outputs to is added to PyskindoseSettings

This solves #42 and part of #22

[codecov-commenter]

Codecov Report

Merging #45 (375dd9c) into master (7a9645c) will increase coverage by 1.78%.
The diff coverage is 88.40%.

❗ Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the Github App Integration for your organization. Read more.

@@            Coverage Diff             @@
##           master      #45      +/-   ##
==========================================
+ Coverage   66.43%   68.21%   +1.78%     
==========================================
  Files          43       52       +9     
  Lines        1585     1699     +114     
==========================================
+ Hits         1053     1159     +106     
- Misses        532      540       +8     

Impacted Files	Coverage Δ
tests/manual_tests/base_dev_settings.py	100.00% <ø> (ø)
src/pyskindose/plotting/create_dose_map_plot.py	25.45% <21.42%> (+1.45%)	⬆️
...skindose/plotting/create_notebook_dose_map_plot.py	25.00% <60.00%> (+5.64%)	⬆️
src/pyskindose/settings/pyskindose_settings.py	81.53% <81.53%> (ø)
src/pyskindose/settings/patient_offset.py	90.00% <90.00%> (ø)
src/pyskindose/settings/plot_settings.py	92.85% <92.85%> (ø)
src/pyskindose/settings/phantom_settings.py	93.75% <93.75%> (ø)
src/pyskindose/settings/translation_direction.py	94.44% <94.44%> (ø)
src/pyskindose/settings/phantom_dimensions.py	94.73% <94.73%> (ø)
src/pyskindose/settings/rotation_direction.py	95.23% <95.23%> (ø)
... and 14 more

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more