Upgrade Apache Commons Collections to v3.2.2

Version 3.2.1 has a CVSS 10.0 vulnerability. That's the worst kind of
vulnerability that exists. By merely existing on the classpath, this
library causes the Java serialization parser for the entire JVM process
to go from being a state machine to a turing machine. A turing machine
with an exec() function!

https://web.nvd.nist.gov/view/vuln/detail?vulnId=CVE-2015-8103
https://commons.apache.org/proper/commons-collections/security-reports.html
http://foxglovesecurity.com/2015/11/06/what-do-weblogic-websphere-jboss-jenkins-opennms-and-your-application-have-in-common-this-vulnerability/

This reverts commit 1bc9c9ac72b55f490b9628628d2dbc2179a86909.

Fix maven build warnings:

 - set plugin versions
 - specify resource encoding

Refactored code to remove warnings

Bump Hibernate from 3 to 4.

Replaced deprecated JDBCTemplate.queryForInt