Allow to copy untouched files rather than rewrite them

Practically we may often want to rewrite only those files affected by reduction and copy the untouched files verbatim to avoid the extensive cost of rewriting. This is particularly excessive as often aggregators with few INSTRUMENT sources will get rewritten while those with many CONTORL sources remain untouched.

This MR adds a flag --output-untouched-copy that allows to automatically make a verbatim copy of untouched aggregator files instead. It only works with --output-scope all --output-layout collection and is ignored otherwise with a warning.