Fixes merge error in gui/application.py

From merge 72477b4b63499a7c349ae3cf734c28aa2452b10a.
Fixes VistrailsApplicationInterface#open_workflow()

It called VistrailsCoreApplication#add_vistrail() with too few
arguments, although that was accepted by VistrailsApplicationSingleton
(gui).
Removes duplicated code from configuration.py
Fixes warnings in vistrail_controller.py
Adds some error checking to the DB layer
Fixes a typo
Adds some error checking to the GUI
Removes obsolete setup_options()

read_options() is used instead, since 'rewrite-startup' was merged in.
Makes applications no longer default on sys.argv

This is similar to b662dffd, re-done for 'rewrite-startup'. It allows
applications to function without ever reading sys.argv, which is notably
useful for the API.
Fixes more issues in core/application.py
Fixes single-instance mode
Do not call mark_list_depth on invalid pipelines

core/vistrail/pipeline.py:
  - mark_list_depth:
    Check for source spec before using it

gui/pipeline_view.py:
  Do not call mark_list_depth on invalid pipelines

Ticket: 887
Removes unused file core/command_line.py

This probably breaks the server, but it should be updated after the
'rewrite-startup' merge.
Fix issue with QFileOpenEvents being triggered

QApplication.__init__ needs argv to contain at least one string

Bug 889
Move Connection.moduleConnection to interpreter

Didn't really make sense to have this on the specification-side,
caused issues with subworkflows
Use source spec in interpreter's make_connection

Required for new list handling?