Bugfixes: do not render entire document from grid_base if embedded, use embedded in published grids, fix permission issue in visualization/saved
Fix naming of install action 'setup_virtual_env' --> 'setup_virtualenv'.
Fix directory variable name in setup_virtualenv.
Allow specifying a specific python version when using setup_virtualenv.
data lirbaries: support for showing deleted datasets in the folderview
UI, published histories: use paging in grid and set num per page to 50 (preventing extremely long load times)
merge
Pep-8 fixes for the tool shd config.
Make checking for for migrated tools when starting the Galaxy server a config setting that defaults to True.  This setting should generally be False only for development Galaxy environments that are often set up from scratch (with new db, etc) and migrated tools are not needed in the Galaxy tool panel.  In those cases where this setting is False, starting a fresh Galaxy instance (with no checking for migrated tools) will be much faster.
For setup_virtualenv: allow specifying to not use requirements file for pip install. Empirically, calling pip install PACKAGE may work better than using a requirements file with some package combinations. Specify a specific log file for pip to use during installation.
Tools API Improvements.
Ablity to require tool for API test. Fix test_index for tool panels containing tools outside a section.
merge default
merge default
Handle changing http protocols in the tool shed registry's password_manager_for_url() function.
More refactoring of tools API test case.
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.
Add simple module verions of validation stuff in base controller.

For reuse outside of controllers (i.e. in dataset collections). Objections to refactoring base controller stuff to use this?