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I believe they are statement groups bounded by INPUT and END INPUT that gather data. Just delete them or comment them out using "/*"
Also, I believe you can define a parameter and use it in an IF/END IF block in the input section to allow controlling for prompting. For example:
INPUT
IF RUN_PROGRAM == TRUE
parameters for input
ENDIF
END INPUT
Yes, the "switch" described by David is probably the very best choice for a few reasons.