Fix server error when getting updates to an installed repository.
Redo 74826a5: Attempt fix of UI problems when collections & datasets in same history have same id.
Approach outlined by Carl, introduces separation between Backbone model id and underlying Galaxy id. Backbone id now includes type in the id. Lots of switching around which id is used where - probably introduces some bugs if I failed to update which id is to be used or switched to wrong one.
Pack scripts.
Rename install_manage.IntallManager to be install_manager.InstallToolDependencyManager and add a new class to the same module named InstallRepositoryManager and move appropriate utility functions into it.  Add a new repair_repository_manager.RepairRepositoryManager class and move appropriate utility functions into it.  Change a log of utility functions that took trans to now take app.
Update LWR client and synchronized modules through LWR changeset 148132f.
Mostly style fixes but also adds ability to configure LWR file staging actions with YAML instead of JSON.
Charts: Minor fixes, hide tooltip, patch nvd3 library
Instantiate the Tool Shed's various tool dependency recipe classes with app so it doesn't have to be passed to functions.
For standardization and clarity, rename Galaxy's UpdateManager to be UpdateRepositoryManager.
Eliminate the use of the repository_util.py module for Galaxy installs from the Tool Shed.
Fix PBS GALAXY_SLOTS configuration for torque environments explicitly defining num slots.
Fix typo in b267ce103960.
Charts: Fix jqplot bar axis
Charts: Fix formatting option
Charts: Pad y axis
Updated tag latest_2014.06.02 for changeset 9b78595ec114
Merge stable.
Charts: Re-add pdf export
Merge
Paired collections: prototype creator modal (accessible from the multi-select commands) allowing the user to create a paired collection
Remove debugging from 4d11f59; add packed script