Allow resolution of relative paths in tool data configuration and loc files.
The string ${__HERE__} will be expanded out to the directory the file (XML configuration or loc) currently resides in.

Along with some changes to planemo to detect test data files (https://github.com/galaxyproject/planemo/commit/a40130417dc1be2da785cd5dff64909986d045a0) - the following picard tweak demonstrates how tool developers could use this to build test cases for cached/index data (https://github.com/jmchilton/picard/commit/4df8974384081ee1bb0f97e1bb8d7f935ba09d73).
Add a table for tracking the history of job states.
Ensure all job state changes will be added to the history state table.
Merged in jmchilton/galaxy-central-fork-1 (pull request #559)

Configuration enhancements aim at enabling tool testing of cached data.
Rename variable for clarity after tools can explicitly create collections.

created_collections is ambigious - these are HDCA for implicitly created collections so renaming this field implicit_collections.
Initial work on tool dataset collection outputs from James Johnson.
Allow tools to produce a fixed number of output datasets for a collection.

Valid for tools such as a FASTQ de-interlacer to produce a pair - but not tools that produce a dynamic number of inputs. So far these tools are unusable in workflows and cannot be 'mapped' over - for instance you cannot take a list of interlaced files a produce a list of de-interlaced pairs.

Rename data_collection element to collection to match pattern already formed in tests.
Add paired collection output test.
Prevent tools producing collections from being used in workflows.

Certainly feasible someday but workflow editor logic will require significant overhaul.
WIP: Allow a known variable number of outputs from collections.

Should allow N->N operations without crazy workflow scheduling.
Model changes to track output collection parts...

Jobs just producing HistoryDatasetCollectionAssociations works fine for simple jobs producing collections - but you don't want to map a list over a tool that produces a pair and produce a bunch of pairs HDCAs and a list:pair HDCA- you just want a bunch of pieces and the one list:pair at that the top.  I think anyway... could totally be wrong.
Allow mapping over tools that produce output collections...

... for 'known' output collections (i.e. not dynamically dicovered - not yet implemented) and only for tool execution. None of this currently works for workflows.
WIP: Collection testing.
Testing output lists.
Another variable rename for clarify.
WIP: Make collection and mapping over collections work at same time, progress on testing.
WIP: collection_creates_list.xml
Initialize ToolOutput to ensure not empty.
Fix for known_outputs.
Clean out collection element dup code.