Remove some unused imports from lib/galaxy/tools/__init__.py.
More PEP-8 style tweaks to lib/galaxy/tools/__init__.py.
Small simplifications to lib/galaxy/tools/__init__.py.
Remove broken method fix_integrated_tool_panel_dict.
As of 5f6c670 (Jan 10, 2014) this does nothing (``if section_value is None`` followed by ``if isinstance( section_value, Tool ):``) and nobody seemed to notice - so I assume it is unneeded. If still needed - someone needs to fix it :).
Slightly rework lib/galaxy/workflow/modules.py for readability.
Rework toolbox 'fix' tool tags when multiple configs are loaded.
Looks like the tool tag stuff still assumed there was just one config file - that said toolbox doesn't have a self.sa_session so I think tool tags are broken and have been for some time.
Refactor tool tag handling out of toolbox.
Pretty sure this had been broken (toolbox didn't have a self.sa_session). Anyway - this probably didn't fix that but at least now the big read tool tag loop is more readable (cyclomatic complexity of that method down from 18 to 12).
Tweak completely broken DataTransfer._execute_workflow to respect toolbox abstraction.
Least of the brokeness at this point I suppose - but I would like to not expose tools_by_id external to the Toolbox.
Start decoupling Toolbox elements from XML (sections+labels).
Just a small tweak and some tests to verify these things can indeed be created from dictionaries. Also slightly simplifies galaxy.tools.
Add comment to auto-generated integrated_tool_panel.xml.

Someone more familiar with integrated_tool_panel.xml should feel free to make this comment sharper - but something is better nothing I think.