Rename a few configuration settings

A few variables that were not search specific had searchapp in
their name. Renamed the variables with the search portion removed.

com.recomdata.searchtool.adminHelpURL -> com.recomdata.adminHelpURL
... -> com.recomdata.contactUs
... -> com.recomdata.appTitle
... -> com.recomdata.largeLogo
Detect incomplete configurations loaded

We know have a magic setting, org.transmart.configFine, which must be
Boolean.TRUE for tranSMART to accept running.

The reason for this is that if the file ~/.grails/transmartConfig has
errors, grails will ignore those errors and continue. The Grails code
indicates tries to log a WARN, but this happens apparently too early
in the boot process and and the logger it uses seems a) to have
onlu a null appender attached and b) its minimum error level is ERROR
anyway.

By placing this property at the very end of the Config.groovy file, we
can be sure that the configuration was completely run.
Improve Config.groovy

This commit includes two changes:
* Make the binding used to run grails-app/conf/Config.groovy available
  to the externalized Config.groovy
  (~/.grails/transmartConfig/Config.groovy). See the comment in the code
  for the rationale.
* Remove some configuration relative to spring security since, for
  better or worse, that was moved to the externalized file.
Aliases message is merely informational

Mark it as such so people don't get confused.
Improve error message
Remove reference to removed properties

They are also not needed anymore since they concern requests to the
i2b2 runtime.
Remove dead JavaScript
Removed config com.recomdata.plugins.pluginScriptDirectory

There's no need for it because
com.recomdata.transmart.data.export.rScriptDirectory
already indicates the same directory.
Deprecate RModulesConfig.groovy
Replace occurrences of nvl() with COALESCE

Because transmart-data does not include definition of nvl(), unlike
transmartApp-DB.
Change the way the dep on servlet 2.5 is declared

The previous method was wrong (the dependency scope should be
provided) and using the Grails setting is cleaner.
We still need the dep on servlet-api after all
Try again: servlet-api must be compile dep

Change its scope to compile, but do not include it in the WAR by
removing the JAR from the staging dir.
Do not use Grails console on Config.groovy

It is not available when running as a WAR. Changed to simple printlns
because having code for detecting the two situations is not worth the
trouble and it would clutter Config.groovy.
Improve conf error message on Bootstrap

Mention the console logging settings can be changed by editiing
$GRAILS_HOME/scripts/log4j.properties.
Change message & test for principal in userlanding
Improve README with installation directions
Merge remote-tracking branch 'origin' into genome-browser-plugin-support