emscope needs output folder switch

[gcohler]

We need the ability to specify the output folder on the emscope commands that produce output files.

It currently goes in the current folder

[biosbob]

to clarify, all emscope commands accept a c, --capture-directory option (default '.') which designates a folder of interest.... that folder becomes the source+sink of all files read+written by emscope.... we do presume that folder (even if empty) already exists....

[gcohler]

understood. I'm suggesting here that a user be able to specify a different output folder from the capture (input) folder,