Changes:

 - Move 'stdin' from being a property of the adapter of a specific input to being part of the global tool adapter, for consistency with 'stdout'
 - Add '--basedir' parameter and resolve relative paths in the input using 'basedir'.
 - Add support for "$job" pointers into the job order, usable anywhere "$expr" is supported.
 - 5 out of 6 conformance tests pass.

If 'order' is the same then cwltool puts tool adapter args before the 'inputs' adapters, but rabix is the other way around (I don't know if that is intentional or just an accident of implementation).  Also, somehow I broke "-I1,2,3,4" parameter, but I'm hoping someone more familiar with the code can fix these two issues.