common input API for workflow element functions

[poldrack]

each elemental function should take the same arguments specifying the different directories or other specs (as defined in the argument spec to be written down shortly)

[poldrack]

spec for common input API:

--basedir: common directory in which all of the data live (e.g. /data/brainsss)
--procdir: directory in which built/processed fly directories live (defaults to /processed)
--atlasdir: directory in which atlases are stored (defaults to /atlas)
--flyname: label for an individual fly (e.g. fly-001)
--dirtype: in {func, anat}
--scan: scan number (e.g. if there are two multiple functional scans, could be 1 and 2) - starts at 1