Fix project modification notifications

[samueljackson92]

There was an issue with application window sometimes not being notified when a workspace changes (for example when it is deleted). I also noticed that opening windows which are not MdiSubWindows will also cause the project to not appear modified.

To test:
This has been changed now so that everything the ADS notifies that it has been changed in MantidUI the project is marked as modified. Also when opening the slice viewer, instrument window, spectrum viewer, and VSI the project will be marked as modified (as they will now be serialised, see issues #16961, #16963, #17368, #17249

Fixes #11605 .

Does not need to be in the release notes.

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Reviewer

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Code Review

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• Does the code conform to the coding standards? Is it well structured with small focussed classes/methods/functions?
• Are there unit/system tests in place? Are the unit tests small and test the a class in isolation?
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Functional Tests

• Do changes function as described? Add comments below that describe the tests performed?
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This causes the project to appear as modified after the ADS changes or
after a window (including windows other than MdiSubWindows) are shown.

[DavidFair]

This now correctly sets the modified attribute and prompts the user to save for the listed examples.