Linting and various cleanup items

[CBroz1]

Submission checklist

• [X] Reviewed all Files changed prior to selecting Create Pull Request.
• [ ] NA: Ran and passed all pytests, and ran the pipeline for features not covered by tests.
• [X] Ran pre-commit checks, including black, flake8, etc.
• [ ] NA: Updated the changelog and if making a new release, updated the version.py.
• [ ] NA: Updated documentation, including concepts.md, tutorials.md, and relevant docstrings.
• [ ] NA:After merge, I will push a new tag to upstream (test* prefix if no new release).

This PR does not add any new features and will not make any differences to the site, so several of the above have been skipped. This PR is submitted to standardize this repo and make my forthcoming feature PR easier to review

Submission details

In this pull request, I make the following changes:

• Standardize file maintenance via a markdown linter and pre-commit checks
  • markdownlint.yaml: specify rules to ignore
  • pre-commit-config.yaml: pre-commit checks including import sorter, black and flake8
• Observe markdown linting. Particularly adding linebreaks after headings and limiting line length
  • changelog, contributing, readme, citation.md, index.md, issue templates - line breaks and line length
  • all notebooks - change from + to - bullets
• Ignore temporary files generated via jupyter - Maybe my local install is buggy? Some of these 'jvsc' files stick around
• Observe black/flake8/isort
  • dockerfile.dev - remove trailing spaces
  • apt_requirements, requirements, all notebooks, pytests, pipeline.py, populate.py - imports sorted by isort
  • all notebooks - apply black to cells
  • setup.py - sort imports, add 'ignore F821' for undefined variable
  • analysis.py - add missing attribute descriptions
• Notebook 7: ca_activity_key -> activity_key
• Changelog - previously, version history was not sequential (0.1.1 -> 0.1.0a2). I've revised the version numbers to reflect a linear history without alpha/beta notation. As none of the changed tags currently exist, this shouldn't conflict with existing releases. After merge, I'll push retroactive tags.