Fixes lots of issues found by my IDE
Marks problems
Removes broken methods that I confirmed are unused
Fixes ModuleRegistry raising MissingPackageVersion

If no version exists, get_descriptor_by_name() is supposed to raise
MissingPackage, apparently.
Fixes passwd being marked as uninitialized

in gui/application.py:
  The logic should always initialize it but moving it should
  remove the warning.
Removed command_line import from application_server.py

command_line.py does not exist anymore. I missed this because the .pyc still
existed and application_server.py is not tested by the test suite.
Fixes DBLocator#parse() broken by cccf158c

"Details to be added later".

I'm unsure whether these "parse" methods are actually used.
Pass on application_server.py
Fixes shell.py

Removes old dead code that was left here for unknown reasons.
Adds py_import to shell.py
Fix abstraction vistrail reference

Moved out of try block because we shouldn't run into MissingPackage
when reading a vistrail.
Fix change_connection by conn -> old_conn

Not sure this code path is ever hit currently since we have factored
everything to add/delete, but keeping in just in case
Get missing options in outupt_config code

OutputModeConfigurationWidget.set_combo_value needs to get options
from the field before using them.
Fix missing output type for brokenbarh plot

We need output_type to be specified to be able to set
properties. Probably should encode this as logic in the generator code
in the future.

Also, regenerate the plot python code and the diff
Sorts configuration documentations
Adds missing simple documentations
Adds to the complete documentations
Merge branch 'fix-config-doc' into 'master'
Comment out ImageOutput registration and add fixme

Issue is that we really want an Image type that might permit in-memory
images to be used here as well so comment this out for now.
Don't alter path in runtestsuite.py if not needed