Removal of Indirect class

Fixed issue with plots being rendered in top left of window

Refs #9968
Added signal connections for Python and message boxes

Refs #9968
Refactor Diagnostics to use plots, etc. in tab class

Refs #9968
Added more universal graphing/plotting to indirect tab

Refs #9968
Fix issue with QWidgets blocking UI

Refs #9968
Update spectra, peak and background min/max from C2E

Refs #9968
Refactoring and improvements to commenting

Refs #9968
Merge branch 'bugfix/9968_refactor_indirect_tabs' into develop