Mantid appears to "save over" previously opened project

[PeterParker]

Reported by Timmy. To reproduce:

• Start Mantid.
• Load a data file into a workspace.
• Do "''File''"->"''Save Project As...''" to save the project.
• Do "''File''"->"''New''"->"''New Project''" to create a new project.
• Note that "''File''"->"''Save''"->"''Project''" is now available as a clickable menu item, even though nothing has been modified since the new project has been created.
• Save the project via this method anyway.
• Close Mantid.
• Start up Mantid again and load the originally saved project via "''File''"->"''Recent Projects''".

The contents of the project will now appear to have been "saved over" as it is now empty. ('''Note: In actual fact the originally saved project can be found, saved in a file named "''[name].mantid~''".''')

[PeterParker]

This issue was originally trac ticket 4233