Add mechanism for input generators to specify a main input file.

The --generate-input output can now contain a "mainFile"
member that contains the filename which should be used to
set the $$inputFileName$$ and $$inputFileBaseName$$ keywords in
MoleQueue.

Change-Id: I7c3aca599c7086d68e5d1bd8f97f3aaea8b18595
Prompt for filename when only saving a single input file.

Change-Id: I88aeb9524eb79a97451436b2a960c2e96b106fbf
Merge topic '111-InputGeneratorFileHandling' into master

7dd4c36d Prompt for filename when only saving a single input file.
51500c3e Add mechanism for input generators to specify a main input file.