Revert "added "./" in front of all non absolute output paths for AFNI"

This reverts commit a2d7aa357274e3a9fda5f2f9f6020ab88173c0b2.
Revert "fixed doctests"

This reverts commit 552fed3a9b61627d62778009a7fc554038b409cb.
added missing copyfile for misbehaving interfaces