Maintain not-indexed points in refined crystal maps

[hakonanes]

Description of the change

This PR ensures not-indexed points in a crystal map are maintained after EBSD refinement (refine_orientation() and refine_orientation_projection_center()). It fixes the issue in #622, reported by @Erlendos12 (thanks).

This fix changes the API of the above mentioned refinement methods in that not-indexed points are kept as not-indexed, instead of not being part of the data (False in CrystalMap.is_in_data) as is the case in the current release. I consider the current behavior as a bug, and will therefore release this change as a patch.

I re-ran and saved tutorials with stored cell outputs affected by this change.

This fix will constitute a new 0.8.4 patch release, released after this PR is merged. I hope to do this before April 5th.

Progress of the PR

• Docstrings for all functions
• Unit tests with pytest for all lines
• Clean code style by running black via pre-commit
• Fix regression where a navigation mask is passed (see e.g. the hybrid indexing tutorial in the docs built from this PR)
• Update changelog
• Update release version

For reviewers

• The PR title is short, concise, and will make sense 1 year later.
• New functions are imported in corresponding __init__.py.
• New features, API changes, and deprecations are mentioned in the unreleased
  section in CHANGELOG.rst.
• New contributors are added to release.py, .zenodo.json and
  .all-contributorsrc with the table regenerated.

[Erlendos12]

Great! This will eliminate having to create masks to remove not_indexed orientations when refining. 👍

[hakonanes]

This should be done and merged soon, so that 0.8.4 is released later today.