Update metadata to refer to Grails 2.2.1
Add dependencies on core-api and core-db
Remove dev env data source configuration

This must come from the out-of-tree
~/.grails/transmartConfig/DataSource.groovy file
Use db-core's getCategories instead of i2b2's
ws
Replace call to Ontology Service's getChildren

with call to Controller::getChildren().
Remove extraneous space

This space was preventing the "Set Value" dialog from showing up when
dragging an ontology node with 'oktousevalue' into the subset inputs.
Whitespace
Whitespace; deletion of commented/unreachable code
Call QueryToolController, not i2b2 (run query)

Some small changes in I2b2HelperService were required in order for the
summary statistics to work correctly. Namely, I2b2HelperService tried to
access the panel_number element, but our queries do not set such an
element.
Whitespace
Whitespace
Make comparison store result id, not master id

Having Comparison store the master id is not conveninent because it
would require exposing the concept of "query master" through the API.

The frontend calls runQueryFromDefinition and that gives back a result
id for each of the sets.
It can then save the selected sets by calling
ComparisonController::save(). Before this commit, this action would
fetch the query master id for the passed result ids. When the comparison
was to be loaded, the frontend would be provided with the master ids and
would run i2b2's getRequestXml_fromQueryMasterId in order to retrieve
the query definition. When replacing factoring our the i2b2
getRequestXml_fromQueryMasterId call, if we were to provide a
corresponding call, we would need an API that exposed the concept of
master id. But that seems unnecessary, at least at this point.

So the Comparisons now store the result id instead and we the API
exposes a method to retrieve a definiton from that result
(QueriesResource::getQueryDefinitionForResult()) instead of from a
master id. That way, we only need the concept of query result.
Replace getRequestXml_fromQueryMasterId call in JS

With call to QueryToolController::getQueryDefinitionFromResultId().
Remove call to Project Management cell

The JavaScript code needs removed a lot of code that's not needed in
the core-integration branch. This change only removes inapplicable code
in the previous hot code path. Stuff like project selection is now
unreachable code. The function names remaning are odd (e.g.
getServices() when we don't get any services).

Anyway, that will be for another day.
Do not do line conversions

I'm all for enforcing line ending canonicity, but unfortunately this was
done incorrectly. Specifically, "* text=auto" was added in
.gitattributes without also doing conversions. As the manpage for
gitattributes (man 5 gitattributes) explains in a note:

  When text=auto normalization is enabled in an existing repository, any
  text files containing CRLFs should be normalized. If they are not they
  will be normalized the next time someone tries to change them, causing
  unfortunate misattribution.

Therefore, whenever I touch a file, I replace it completely. Worse, it's
impossible to revert the file to a clean state without uncommenting the
line in .gitattributes.

Because I am unwilling to change all the text files to introduce
normalization, I'm instead changing .gitattributes.
Add new icons for Survival Analysis aCGH GUI
Set icon and class for high dim nodes
change some styling for input panel in Survival Analysis aCGH page
add new definition styling for new button