More ToolPanelManager unit testing.
Eliminate repeated nested object access in ToolPanelManager.remove_guids.
Reduce duplication/complexity in tool_panel_manager.py.
Big conditional in remove_guids switched on sectioned versus un-sectioned with very little difference in what was actually being done. This reduces the cyclomatic complexity of that method from 35 down to 26 (though it is still the most 'complex' method in that file by a wide margin).
Abstract out ToolBox internals from tool_shed.util.tool_util.
Instead of reloading upload actions at this level and exposing tools_by_id - move this logic into the ToolBox in a new method called handle_datatypes_changed().
Centralize abstraction for removing tools from toolbox.
Shield's toolbox.tools_by_id from lib/tool_shed/galaxy_install/tools/tool_panel_manager.py.
Eliminate walking over tools_by_id externally from toolbox.
Abstractions for registering tools from outside toolbox.
Part of effort to further limit exposing tools_by_id directly outside Toolbox.
Eliminate direct in/get checks against toolbox.tools_by_id - use get_tool or has_tool.
Introduce abstraction to prevent lib/galaxy/workflow/modules.py from needing tools_by_id.
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.
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.
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.
Move more logic into ToolSectionElements, raising level abstraction in Toolbox.
Replace another repeated idiom in Toolbox with higher level method in toolbox.panel.