Fix for handling complex repository dependency definitions that contain recipes that include <package> tag sets that define dependencies needed only for compiling the dependent package.
Improved (different at least) extra_files_path handling for dataset outputs.
$output.extra_files_path will now mimic $output.files_path behavior - writing these files to the working directory to have them copied over later. This is more correct when using outputs_to_working_directory, running jobs as the real user, running jobs through LWR/Pulsar, or when using the NestedObjectStore. This is less efficient the 90% of the time when none of these conditions hold.

There is still an open issue that for inputs -  $input.extra_files_path returns a non-exist path for DiskObjectStores but throws an error for NestedObjectStores. This behavior could be synchronized by this patch (https://gist.github.com/jmchilton/d05bcf02874762cdb829) - though I do not know if this is the intended behavior of NestedObjectStores.
Add a few more comments about dataset path rewriting in the dataset wrapper.
Charts: Allow empty columns
Charts: Connect data points with template url
Charts: Fix last change
Fix for interpreter on version commands (when different from command interpreter).

Thanks to Will Holtz for tracking down the problem and Peter Cock for submitting the patch.
Add a dependency manager with tag attribute handler classes to manage the process of populating and unpopulating the toolshed and changeset_revision attributes for <repository> tag sets when uploading and importing / exporting repositories from the tool shed.
Move 2 Tool Shed utility functions into the middleware hg class.
Eliminate the use of trans when exporting repository capsules from the Tool SHed and move the new tag_attribute_haldler.py module where it was meant to be located.
A bit of repository dependency function re-factoring for Galaxy installs.