Update:
I have changed the permissions on all data files/directories to do with the Godot program and where I have my project to ensure my user and group authorities have full permissions. I can now start Godot from the terminal without needing to invoke superuser, however, in the terminal I am now getting the following, which might be related to the original problem:
ERROR: save: Condition ' err ' is true. returned: ERR_CANT_OPEN
At: core/io/resource_format_xml.cpp:2725.
ERROR: save: Can't Save!
At: tools/editor/editor_settings.cpp:441.
ERROR: save: Condition ' err ' is true. returned: ERR_CANT_OPEN
At: core/io/resource_format_xml.cpp:2725.
ERROR: save: Can't Save!
At: tools/editor/editor_settings.cpp:441.
Godot seems to be working however, so I am not sure if the above are anything to be worried about.
Thoughts?