Automatic indexing of un-indexed files

[vkbo]

Summary:

This PR adds automatic indexing of un-indexed files. This replaces the potentially fragile check of comparing all files to the current index. The new implementation is also silent, aside from some info printed to the status bar.

Related Issue(s):

Reviewer's Checklist:

• The header of all files contain a reference to the repository license
• The overall test coverage is increased or remains the same as before
• All tests are passing
• All flake8 checks are passing and the style guide is followed
• Documentation (as docstrings) is complete and understandable
• Only files that have been actively changed are committed