Tool Dependencies: Convert James Taylor's dependency testing file lib/galaxy/tools/deps/tests.py into a formal unit test.
Tool Dependencies: PEP8 fixes for lib/galaxy/tools/deps/__init__.py
Tool Dependencies: Add tests for addditional existing behavior for tool dependencies.
Drop multiple tool_dependency_dir implementation for now.

I like the ideas, but I will circle back around to it once I have implemented more granular, plugin style tool dependency resolvers. They will benefit from there being 1 default_base_path, but allowing it to be overridden on a per resolver basis.
Tool Dependencies: Small clean ups.
Tool Dependencies: Begin rearranging arguments so all ones not of interest to every potential dependency resolution plugin can be kwds
Tool Dependencies: Finish refactoring toward generic keyword arguments.
Tool Dependencies: Introduce the concept of a dependency resolver, DependencyManager will check each in turn.
Tool Dependencies: Refactor common code out of _find_dep_versioned and _find_dep_default.
Tool Dependencies: Split package resolvers into Tool Shed and traditional Galaxy versions.