PEP-8 fixes to lib/tool_shed/galaxy_install/install_manager.py
PEP-8 fixes to lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
PEP-8 fixes to lib/tool_shed/galaxy_install/repair_repository_manager.py.
Make it clear repository_dependency_manager doesn't use ToolSection objects.

Just wants the keys.
Update repair_repository_manager.py to make clear it is not using ToolSection directly.
More centralization of code for registering tools in ToolBox.
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).
Eliminate one reference to ToolBox.tool_panel in install_manager.py.