Fix server error when attempting to update a repository that defines set_environment tool dependency types.
Jobs - Convert job_script's env_setup_commands to list.
Jobs - Allow destinations to declare arbitrary envirnoment variables.
See job_conf.xml.sample_advanced for examples.
Extend destination specific env options.
Add support sourcing files and executing arbitrary shell commands (see documented examples).
A bit of rework for recently introduced assert action types for tool dependency package install recipes: 1) assert_file_exists - true for both files and symlinks, but false if path is a directory 2) assert_file_executable - true for both files and symlinks but false if path is a directory 3) assert_directory_exists - true for both directories and symlinks, but false if path is a file 4) assert_directory_executable - true for both directories and symlinks, but false if path is a file.
Fix for the install_repository_revision function in the Galaxy API: a more correct and informative message is now displayed if any of the request parameters is invalid.
Reorder eggs.require for some fabric files.
Merged in jmchilton/galaxy-central-fork-1 (pull request #378)

Allow specification of environment variables for job destinations
Fix spelling. Good catch by Nicola.
Twill test framework cleanup. Update install and test methods to reflect changes in base twilltestcase.py.
Create run_tests.sh to replace run_functional_tests.sh
Should be backward compatible but features better argument handling - things can appear in other orders (-id x -data_managers is the same as -data_managers -id x for instance), better error messages if arguments are missing, and more standard short argument with single dash or long argument with double dash variants of each argument are available.
Add unit tests to run_tests.sh.
Add qunit test options to new run_tests.sh script.
Can target specific tests or all tests and can optionally watch tests using Carl's work on 'grunt watch'.
Rework test framework testing and tools.
-framework will still cause just a small set of non-default, non-user facing tools to be tested and exerise various aspects of the tool and test frameworks, but now an argument can be passed in -with_framework_test_tools to allow these tools to be used as part of the normal test framework (i.e. when not using -framework). This serves two purposes - to ensure the feature coverage of existing tests remains high as the tests are migrated out of the distribution and to allow a set of tests to be available for functional (e.g. API tests) that users don't need to see.
Fix for DatasetListWrapper.
Merge fix from stable.
Record history content type with output of history contents API.

Downstream in dataset collections branch this isn't just dataset, including this will allow clients to distinguish between different kinds of content.
Refactor backbone models to allow different kinds of history contents.

In particular, add a new backbone parent model (HistoryContent) refactored out of HistoryDatasetAssociation. This makes room for a forth coming HistoryDatasetCollectionAssociation model that will be emitted from the history contents API.

There are likely better ways to share common functionality between a dataset and a dataset collection contents - more JS savy developers should feel free to refactor into smaller mixins for instance. For now HistoryContent is just composed of the overlap in functionality between dataset and collection representations downstream and is an quick and dirty way to share said functionality.
Refactor backbone views to allow different kinds of history contents.

This makes room for a forth coming HistoryDatasetCollectionAssociation model that will be emitted from the history contents API. Same comment as previous changeset applies - this is a potentially crude way to share duplicated functionality and a better design would be most welcome.
Rename historyPanel.refershHdas to refreshContents.