Decide how arguments files should work and implement/uncomment that code

[tfenne]

I personally favor mimicking Python's argparse for this where, instead of having a special option for it, e.g. --arg-file=foo.txt we use a special symbol to indicate that an argument is expected to be a file and it's token on the command line replaced with tokens from the file, e.g. --foo 1 --bar 2 @args.txt.

Further, the way argparse treats each line in the file as if it where a single token, wrapped in quotes on the command line, which has some nice benefits. I.e. if you are passing many option that would otherwise need to be quoted, you don't have to worry about it, e.g.:

--samples
MySample
Some Stupid Sample
Who Put Spaces In Sample Names

[tfenne]

Done, see PR #71 .