Added sqlite metadata detection (from JJ)
Merged galaxy/galaxy-central into default
Restructure tool external file logic in load_tool_from_tmp_config in ToolValidator...
... so internals of tool XML description are only utilized in the galaxy.tools module (and submodules). Add some unit tests for this new method for finding externally referenced files.
Fix new Tool.get_externally_referenced_paths to find imported macro files.
Should fix this bug https://trello.com/c/TeguDYSq discovered by Bjoern... on stage at the GCC.
Trackster: fix single-pixel gap bug in quantitative track display.
Merged in jmchilton/galaxy-central-fork-1/next-stable (pull request #449)

Fix tool shed's logic related to finding tool externally referenced files.
Merge next-stable.
API tests for authenticate and some of users endpoints.
Introduce ApiKeyManager to replace and expand upon CreatedApiKeysMixin.
Add get_api_key helper method to visualization templates.
For use in the IPython visualization plugin - improves abstraction level and likely allows users who have never created a key to use IPython visualization.
Plugin framework: Expose plugin path to mako templates.
Allows plugin templates to utilize resources contained in the plugin. Requested by Eric - should clean up IPython plugin somewhat.
Merged in iracooke/galaxy-central (pull request #446)

Metadata detection for sqlite datatype
Fix for writing entries to shed_tool_conf.xml so that sym linked files are handled correctly (thanks Bjoern), and making changes to this and data manager config files thread-safe.
Merged next-stable
Merged in jmchilton/galaxy-central-fork-1 (pull request #450)

Plugin framework enhancements to improve galaxy-ipython.
Fix-up citation related GUI.
Was displaying warning message about history citations being potentially incomplete for tools - which if they have annotated citations we should assume they are complete.
Pack scripts.
Merge next-stable.
Add annotated citations for MAF tools.

Add macro file to centralize this and in help citation description as well.
Add annotated citations various tools.