Added missing connections to topup workflow

Encoding direction and readout time were missing
Merge branch 'enh/NewPreprocessDMRIWorkflows' into unstable
Improvements on TOPUP and related workflow
New eddy interface (nipy/nipype#662)

* New interface for eddy. NO TESTING HAS BEEN DONE, though
* Added interface.cmdline on documentation comments
Added dumb files for interfaces
Merge branch 'enh/NewPreprocessDMRIWorkflows' into unstable
Checked that eddy.cmdline works

Added Eddy to __init__
Fixed minor typo in documentation comments.
Merge branch 'enh/NewPreprocessDMRIWorkflows' into unstable