Standardize formatting and fix Codacy errors

[troyraen]

Completes #99

Done, just waiting for testing.

• Enable branch protection rules on master and develop. Merge requirements: PR, 1+ Approval (master requires approval by a code owner), Codacy Static Code Analysis passes.
• Add file .pre-commit-config.yaml to enable the use of pre-commit Git hooks. Its use will be optional. To use it, first install pre-commit with pip install pre-commit, then each time you clone the repo, install the hooks defined in the config file with pre-commit install (in the repo's top-level directory).

Python files:

• Run black
• Reorder imports
• Fix spacing, fstrings, docstrings
• Use snake case, raise from, isinstance instead of type, is not instead of !=
• Remove unused variables. Use list and dict constructors instead of comprehension. Avoid bare except.
• Disable Pylint warnings of things that won't be fixed

Shell files:

• Standardize formatting (quotes, brackets, etc.)
• Run beautysh
• Add missing variables and remove unused ones
• Use -r with read to avoid mangling backslashes
• Avoid cd when possible, else add || exit to exit on failure

Markdown files:

• Fix issues that Codacy complains about in Markdown files
• Run mdformat on all markdown files

Finally:

• Test (esp. f91ee36)