Light refactoring

[sfmig]

A first chunk of light refactoring:

• an example of avoiding long parameter list
• reorganised the directories (moved bash scripts, guides and notebooks to the root level)

I figured we could merge to main this new structure and then I continue with closing currently open PRs.

Next steps towards that:

• add stereo-calibration work (as it is in current state)
  • PR Timecodes matching #2
• add bash scripts:
  • to run video reencoding (PR Bash script to reencode videos #31)
  • to run reencoding+frame extraction (PR Frame extraction with reencoding #78)
• add/update guides
  • PRs How to create GIN private repo for crab data #81,
  • PR Update extract frames guide #75
• add exclude pattern feature to combine annotations, with tests
  • PR Add exclude pattern to combining annotations #77
• finish test for frame extraction
  • PR Tests for frame extraction #24

[codecov-commenter]

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (3665608) 29.81% compared to head (13093bb) 29.81%.
Report is 1 commits behind head on main.

Files	Patch %	Lines
...bboxes_labelling/combine_and_format_annotations.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #86   +/-   ##
=======================================
  Coverage   29.81%   29.81%           
=======================================
  Files           6        6           
  Lines         332      332           
=======================================
  Hits           99       99           
  Misses        233      233           

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