Refactor control of long-running external processes in GUI

[tturocy]

This refactors and improves the control of long-running external processes.

• Clarifies the difference between the monitor dialog and the actual controller of the external process
• Makes the handling of the external process more robust
• Moves parsing of external process output into the process handler rather than the analysis output.

This is preparatory work which will enable the ability to run long-running processes as threads.