Update code checks and documentation after commit 17a2dc7.
Backport CLI-manager infrastructure from LWR.
I had previously reworked this CLI stuff to work with LWR - this changeset brings those changes back to Galaxy. This version has the advantage of using the job script module - the upshot is that GALAXY_SLOTS, job_conf env directives, and job metrics should all be usable now with the CLI runner. This version also has a local shell variant (to eliminate the use of SSH and run qsub directly on the same machine), a variant of the Torque executor to target slurm's torque compatibility executables (doesn't support -x), and some other small bug fixes.
Merged galaxy/galaxy-central into default
Merged galaxy/galaxy-central into default
Workflow API: Add documentation for dataset_collection_ids param.
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....
Merge pull request #383.
Re-update documentation for fixes in a44bea8.
Merged in jmchilton/galaxy-central-fork-1 (pull request #385)

CLI Job Runner Enhancements
Add framework test tool that has both data and data_collection param - with test case.

Tool test is mildly useful to verify this works for single execution - but more useful as basis for future changesets testing mixed collection and subcollection mapping tool executions.
Bugfix: Don't require matching identifiers to match up collections.

I changed this in some other places in the code before committing but this part stayed broken. Collections will match on order, type, and number of elements (pushing the problem to UI) - element identifiers can be different but will be preserved when possible.
Bugfix: Rework collection matching logic so it properly matches combined collection/subcollection mapping.

With functional test to verify it works end-to-end with tool execution and unit tests to verify different kinds of collection combinations.