Separate output file directory

[vsilwal]

It would be better to have a separate directory for all the output files generated, and keeping the data directory unchanged.

[vsilwal]

Even better would be to have four separate directories:
(1) Data (extracted waveforms);
(2) RTZ waveforms;
(3) input weight files;
(4) output files

[vsilwal]

We need to work on output filenames. Only FMT solutions should have*_fmt.
I am posting this here since we would also want a separate results directory.

[celsoa]

I think the directory structures will become clear when we finalize workflows for DC and FMT. See also #24.