Fixes VisTrails messages hitting the root logger

New IPython version might set up a root logger. Its StreamHandler would
thus handle VisTrails messages alongside our own handlers.
Fixes CLTools not setting stdout/stderr if empty

Returning None instead of a file breaks type safety and will make
pipeline fails.
Merge branch 'v2.1' into 'master'

Conflicts:
	vistrails/core/debug.py
Fixes code issues in gui.application

Still missing VistrailController import.
Adds context menu to reload CLTools modules