Bugfix: galaxy.workflow.extract expects hids - API was consuming encoded ids.
API now properly expects hids. That was unfortunate - need to figure out why the existing functional test did not break because of this and improve it.
Bugfix: Track collection_type when extracting collection inputs from histories.
Add functional test to verify the correctness of this tracking.

TODO: refactor __skip_unless_tool from tools test so this new workflow test can be skipped if not run with -with_framework_test_tools.
Improve API test skipping when required tools are absent.
Replace ad-hoc tools API test method for skipping tests with a more general purpose decorator. Use new decorator to specify required tools for workflow tests.
Expose use_remote_user via configuration API.
Attempting to improve automated testing... marginally.
Fix type introduced in renaming the InstallManager to the ToolMigrationManager - thanks Nicola Soranzo.
Force an absolute path for the temp directory in the local runner
Force an absolute path for the temp directory in the local runner
pep8 fixes
Merge stable.
Merge.
Simpler, more powerful subcollection mapping.

Collections can be mapped over 'data' parameters and sufficiently nested collections can be mapped over 'data_collection' parameters (for instance a list of 5 pairs can be supplied to a tool taking in a pair and 5 jobs will be executed). I (perhaps poorly) term these concepts collection mapping and subcollection mapping.

Prior to this changeset - the API for doing collection 'mapping' and 'subcollection mapping' was somewhat more divergent and the tool execution code explicitly forbid doing both kinds of mappings in the same tool execution even if the effective collections could be matched (e.g. it could not map a 'data' parameter over a list of 5 datasets and a pair parameter a list of 5 pairs in the same execution).

This changeset should remedy this - as long as the effective collection mappings can match up such jobs should be possible. The workflow editor (and I think runner) already thought this was possible, so this changeset reduces the tool-workflow impedance mismatch - an existing problem exacerbated by recent dataset collections introduction.

This all needs much more testing - test workflows execute this way, functional test of a tool execution that combines collection mapping and subcollection mapping, etc....