More PEP-8 style tweaks to lib/galaxy/tools/__init__.py.
Small simplifications to lib/galaxy/tools/__init__.py.
Simplify toolbox.load_tool_tag_set method.

guid is taken as input but is always produced the same way from the same input, so just derive it inside the method instead.
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 :).
Introduce ToolPanel abtraction.

There are some repeated operations on an odict in Toolbox that could be cleaned up (fewer lines of code, more readable) with new abstraction in place. Starting with __add_tool_to_tool_panel but will work its way to other methods in Toolbox eventually.

Abstraction reduces cyclomatic complexity of Toolbox.__add_tool_to_tool_panel from 23 down to 18.
Introduce new abstraction of tool lineages.

 - Don't force non-toolshed tools into the tool shed install database.
 - Abstract out dealing with the tool shed install database from toolbox, to potentially allow other tool lineages implementations.
Hide details of toolbox.tools_by_id from lib/tool_shed/util/tool_util.py.
Shield toolbox.tools_by_id from lib/tool_shed/galaxy_install/tools/tool_panel_manager.py.

Reuse remove_tool_by_id abstraction setup for data managers.
Another use of remove_tool_by_id abstraction.
Abstractions for registering tools from outside toolbox.

Part of effort to further limit exposing tools_by_id directly outside Toolbox.
Slightly rework lib/galaxy/workflow/modules.py for readability.
Introduce abstraction to prevent lib/galaxy/workflow/modules.py from needing tools_by_id.
Tweak completely broken DataTransfer._execute_workflow to respect toolbox abstraction.
Eliminate direct in/get checks against toolbox.tools_by_id - use get_tool or has_tool.
Eliminate walking over tools_by_id externally from toolbox.
Rebase.
Rebase.
PEP-8 comments in lib/galaxy/tools/__init__.py.
Move more logic into ToolSectionElements, raising level abstraction in Toolbox.
Rework toolbox fix tool tags when multiple configs are loaded.

Looks like the tool tag stuff still assumed there was just one config file.