Change Output Naming Behavior

[galaxnet]

Output behavior currently overwrites old output without warning. Please remedy this to address issues with batch runs of the software.

[gorzek]

What do you want the behavior to be? Could be any of:

• Prompt to confirm an overwrite.
• Automatically increment a number at the end of the output filename (adding such a number if not already present).
• Adding such functionality to the runs flag, adding a new split option which puts every run in a new file.

The second and third would be separate workflows and both would eliminate the need for a prompt.