[RTM when tests pass] Reorganize files

[Ipuch]

Reorganize files to be more efficient at finding files.

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This change is 

[codecov]

Codecov Report

Attention: 76 lines in your changes are missing coverage. Please review.

Files	Coverage Δ
bioptim/__init__.py	100.00% <100.00%> (ø)
bioptim/dynamics/configure_problem.py	71.00% <100.00%> (ø)
bioptim/dynamics/dynamics_functions.py	84.29% <100.00%> (ø)
bioptim/dynamics/integrator.py	95.97% <100.00%> (ø)
bioptim/interfaces/abstract_options.py	100.00% <100.00%> (ø)
bioptim/interfaces/ipopt_options.py	100.00% <100.00%> (ø)
bioptim/interfaces/solver_options.py	100.00% <100.00%> (+15.55%)	⬆️
bioptim/limits/constraints.py	51.40% <100.00%> (ø)
bioptim/limits/multinode_penalty.py	62.20% <100.00%> (ø)
bioptim/limits/penalty.py	83.53% <100.00%> (ø)
... and 20 more

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[pariterre]

Reviewed 35 of 35 files at r1, 2 of 2 files at r2, all commit messages.
Reviewable status: complete! all files reviewed, all discussions resolved (waiting on @Ipuch)