Fix minor issues and clean up class inits

[vkbo]

Summary:

This PR fixes an issue with idle time not being reset when creating a new project, removes the context menu from the main window, and cleans up class initialisation in the code base. The last one fixed a few errors as well.

Related Issue(s):

Resolves #1149
Resolves #1147

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