Update galaxy tool components with changes to enable planemo.

galaxy/tools/deps/brew_exts.py

galaxy/tools/deps/brew_util.py

galaxy/tools/deps/commands.py

galaxy/tools/deps/docker_util.py

galaxy/tools/deps/dockerfiles.py

galaxy/tools/deps/resolvers/homebrew.py

galaxy/tools/lint.py

galaxy/tools/linters/__init__.py

galaxy/tools/linters/citations.py

galaxy/tools/linters/help.py

galaxy/tools/linters/inputs.py

galaxy/tools/linters/outputs.py

galaxy/tools/linters/tests.py

galaxy/tools/linters/top_level.py

galaxy/tools/loader.py

galaxy/tools/loader_directory.py