Emit clear index signal when project is closed

[vkbo]

Summary:

This PR adds a call to clear the index when a project is closed so a indexCleared signal is emitted. This clears the reference panel. The panel is anyway rebuilt when a new index is loaded, but only if there are any tags defined, which leaves data behind if the next project opened doesn't have any.

Related Issue(s):

Closes #1718

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