Allow usage of @Autowired in the CLI definitions since they are loaded
as beans.

Deprecate most of the AbstractSpringAwareCLI logic since it can now be
done via annotations.

Use ApplicationContext in GemmaCLI and SpringContextUtil so that we can
reuse the component scan logic via getBeansOfType.

Merge workerContext with cliContext as we don't need to make
distinctions between the two.

Unfortunately, it appears that this error arises when there is high
contention on this specific call.

Inline removeForExperiment() to make sure that findByInvestigation() and
remove() happens in a single transaction.

…gent transaction isolation level

This essentially locks the database to prevent dirty read. It's not
ideal, but it fixes the problem in a definite manner.

Revert some changes in 4cfb329 since we
don't need to deal with StaleStateException anymore.

Relates to #400.

Use a finally block to close the scrollable results.

Replace two unnecessary usage of scroll() that should be simplified by
a more efficient list() call.

update home page slide show to show only database stats
hide diff ex and coex search from home page
hide some features from navigation menus
gene page some tabs and some details hidden
remove social media link
update copyright date
refer to #154

Only include tests marked by the UnitTest category for
maven-sure-fire-plugin.

Include all test ending with Test.java and exclude those marked by the
UnitTest category for integration tests.

Use integration-test and verify goals for maven-jasmin-plugin as it
require a fake browser.

…egration-tests

Use maven-failsafe-plugin to handle integration tests

Only retain the taxon-based constructor that lookups the configuration.

Move commons-io to the root pom

Related to #259 although we haven't changed the package naming yet.

Fix typo in PubMedSearchTest test name.

Make it an error to pass -testing/--testing in the command arguments.

Move all cache configuration in ehcache.xml.

There's no point in caching entities that are only by users and admins
in very specific contexts and that should always be fresh.

Check if the cache is an Ehcache before casting it.

Remove unused Terracotta section.

Properly escape HTML entities when generating stats.

Those resources were relocated to be properly namespaced in gsec JAR.

Hibernate 4 uses that information to truncate fractional seconds
accordingly. We want to preserve the milliseconds of the java.util.Date
object, so 3 is adequate.