Reduce technical debt of ATOCA/SOSS extraction code

[stscijgbot-jp]

Issue JP-3755 was created on JIRA by Tyler Pauly:

The implementation of the ATOCA algorithm for NIRISS SOSS spectral extraction was a large task, and many aspects of the project were left uncompleted. This ticket is being filed to address a variety of issues remaining with the code:

No unit tests
Lack of documentation
Stale code/TODOs abound
Some refactoring would likely improve performance and definitely improve readability