rebased command line arguments (CLA) stuff

outsourced CLA-registrations to arguments.py; included
classmethod-decorator; completed comments
CLOSED - task 10: Clean main directory 
http://github.com/gnudo/grecoman/issues/issue/10
file renaming
added Merlin functionality to GUI
and reserved "target" property for future implementation of Merlin
outsourced checkAllParameters method
reduced redundant methods
further reduction of redundant methods
outsourced also getComboBoxContent method
ideally, in main.py only those methods should stay that are directly
affecting the GUI (however, it's not consistent yet)
added new menues to UI
44: Add possibility to load only specific parameters 

Task-Url: https://github.com/gnudo/grecoman/issues/issue/44
finished documentation in fileIO.py;
removed "lastdir" property from being updated when loading template
files
added automatic change to AFS as computation source when submitting to
Merlin
added correct tabulator-ordering for GUI fields and fixed a few bugs

FIX: increased waiting time for loading new slice (e.g. when cons-2 is
really very slow); grecoman local caller script now working
CLOSED - task 46: include try/catch in loading of config-files 
http://github.com/gnudo/grecoman/issues/issue/46
CLOSED - task 45: separate internal "lastdir" variable 
http://github.com/gnudo/grecoman/issues/issue/45
added Merlin-compatibility to singleSliceFunc and target-specific flag
next steps towards full Merlin compatibility

ADD: full Merlin compatibility for singleSlice (added methods for
ssh-connection with Public key auth, directory path rewriting etc.)
MOD: probably broken compatibility with submitting full jobs to
pieple (not tested yet)
merged newest changes to development branch
merge of the latest bugfix after discussion with anne
added ROI-selection possibilty in sinogram-creation;
added submit-to-merlin method in job-submission (but paths are not yet
correct for all "actions")