Update all dependencies

Use pavlab-starter-parent to manage common dependencies with other
Pavlidis Lab projects.

Add missing <scm/> and <issueManagement/> entries in pom.xml.

Use Hibernate 3.6.10.Final and remove ehcache dependency since we don't
use it directly (it is still imported through hibernate-ehcache).

Use gsec 0.0.7 and update context configuration loading accordingly.

Use commons-pool2 and modify data source configurations accordingly.