Fixes for over escaping in c2bed0a.

Fixes dozens of tool functional tests.
Merge next-stable.
Add --no_cleanup option to tests.
Skip checking tool migrations for Galaxy in tool shed tests.
Fix remaining tool shed test cases for new escaped values.
I think in this case the values on the page are correct now - but the test framework needs to be updated to handle the escaped value.
PEP-8 fixes for a few Tool Shed install components.
 - lib/tool_shed/galaxy_install/install_manager.py
 - lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
 - lib/tool_shed/galaxy_install/repair_repository_manager.py
Tweak two ToolShed modules to clarify they don't use ToolSection...
... objects (directly anyway). I would like to refactor all the tool shed components to not deal directly with ToolSection objects but instead just pass around IDs.
More centralization of code for registering tools in ToolBox.
Eliminate one reference to ToolBox.tool_panel in install_manager.py.
Simplify shed-y logic in load_tool_tag_set.
Drops cycolomatic complexity from 14 to 10 for that method.
De-duplication for loading elements into the tool panel.
Create one public method load_item on ToolBox that should be used externally instead of load_tool_tag_set, load_section_tag_set, etc.... This reduces the duplication within the toolbox and between the toolbox and the Tool Shed's ToolPanelManager. Probably more importantly it also is another step down the road toward hiding implementation details such as toolbox.tool_panel and toolbox.intergrated_tool_panel from the ToolPanelManager.

Already had unit test coverage for ToolPanelManager stuff here - but added test coverage for loading labels, workflows, and tool directories.
Abstract tool lineage handling out of ToolBox.

Start work on infrastructure to support tool lineages not defined within the tool shed install model.
Helper methods on ToolBox to abstract away lineage details.

Reduces code duplication slightly and simplifies __add_tool_to_tool_panel (cyclomatic complexity reduced from 20 to 14).