Make all params and models lower-case

[tsalo]

Closes #81 and closes #70. All of the params and models in the BEP016 doc are lower-case so this might fit better.

Changes proposed in this pull request

• Rename models and params in config files to be lower-case.
• For any models or params that are defined within the workflows, make them lower-case and remove any non-alphanumeric characters automatically.
• Remove non-alphanumeric characters from bundle entities.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 12.50000% with 7 lines in your changes missing coverage. Please review.

Project coverage is 33.67%. Comparing base (f20d5ac) to head (6e5d9ea).

Files	Patch %	Lines
qsirecon/utils/misc.py	25.00%	3 Missing :warning:
qsirecon/workflows/recon/dsi_studio.py	0.00%	2 Missing :warning:
qsirecon/workflows/recon/mrtrix.py	0.00%	2 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #90 +/- ## ========================================== - Coverage 33.69% 33.67% -0.03% ========================================== Files 56 56 Lines 6914 6922 +8 Branches 907 907 ========================================== + Hits 2330 2331 +1 - Misses 4481 4488 +7 Partials 103 103 ```

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