Add an API to remove items from tool data tables
Merged galaxy/galaxy-central into default
Removed blastdb_p.loc.sample, moved to tool-shed repo
fix method names and api doc
Add SQlite dataproviders: SQliteDataTableProvider - Allows any query to be run and returns the resulting rows as arrays of arrays, SQliteDataDictProvider - Allows any query to be run and returns the resulting rows as arrays of dicts
Add dataproviders to the SQlite dataype
Remove incorrect usage of threading.Lock().
Not sure what the intention was - but the Lock is created locally in the function so nothing else would be waiting on that particular lock.

At some point we may wish to revisit other usages introduced in 1bb04279216e0abf4e24b9299cccc06c10b9c0ac.
Improvements to loading help text from tools.
Do not convert rst to a mako template until needed, this is a costly operation and has the potential to speed update Galaxy start time. Move logic related to parsing of simple help text blocks out of tool and into the new tool parser interface and add implementation for YAML-based tools as well as unit tests for both. More advanced, multi-page tool help is still possible, workflows with the old tool form, but is only available to XML-based tools.
PEP-8 fixes for lib/galaxy/tools/search/__init__.py.
Bugfix and enhancement related to indexing tool help in tool search.
Added a config option for disabling indexing of tool config. This combined with the previous commit, shave over a second off (slightly more than 25%) Galaxy's startup time for the default toolbox on my laptop. Enable this option for functional tests - which will likely never care about seaching this index.

When I went to test this - I noticed that searching wasn't actually working for help messages - this is because tool.help is not a string but a mako template - so I switched it over to render the page and stick it in the whoosh index instead of probably some default to string object pointer or something.
Fix bug with watch tool config option parsing.
Remove another incorrect lock statement.
Fix bug in registry.py requiring the odd relative import of locally defined data type modules.
So many times I helped people get stuff working by telling them to stick the import in this file without ever understanding why the import needed to be there, the answer would appear to be - because there was a bug.

Kanwei Li fixed the same bug in the sniffer code in d7c529f.

Fixing this bug should allow dynamically injecting datatypes (outside context of tool shed) without modifying Galaxy's source - important for OS packages and planemo.
Allow specification of multiple datatypes_conf.xml files.
If there are conflicting datatype registrations - the registration that appears last in these files will be used. There is an open issue here regarding order of sniffers. This is going to just piggy back on whatever the tool shed would do - so however we decide for instance to resolve sniffer orders in that respect will work with this mechanism as well.

For now though - lets just specify that the best practice should be to just place all non-shed sniffers in one file if specifing multiple datatypes configurations manually like this.
Merged in lance_parsons/galaxy-central-pull-requests/blastdb_p.loc.sample (pull request #605)

Removed blastdb_p.loc.sample, moved to tool-shed repo
Merged in abretaud/galaxy-central (pull request #577)

Add an API to remove items from tool data tables
Allow multiple tool data table config files...
... use this functionality to implement tests for tool data API.
PEP-8 fixes for lib/galaxy/tools/data/__init__.py.
Small improvements to tool data API.
Update tool data API to use newer API decorator for better error handling, create some abstractions for reuse down stream, etc...
Implement a detailed break down of data table fields via API.
Originally this approach was laid out by Kyle Ellrott in this pull request (https://bitbucket.org/galaxy/galaxy-central/pull-request/531/add-downloads-to-tool-data-api/diff). The changes to galaxy.tools.data are entirely his contribution, I only reworked the API and endpoint slightly and did some stylistic fixes and refactoring.