Documentation for JIRA 4.0. Documentation for other versions of JIRA is available too. 
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To make any substantial modifications or additions to JIRA's source, you should read Building JIRA from Source. This implies building a WAR distribution and deploying this to your Application Server.
This guide describes how to make a source code modification to a single class file.
maven idea
maven eclipse
To deploy a patch, drop the file in the classpath from <jira-install>/atlassian-jira/WEB-INF/classes. For example, if you compile the class:
com.atlassian.jira.appconsistency.integrity.check.SearchRequestRelationCheck
It'll be available from:
/target/classes/com/atlassian/jira/appconsistency/integrity/check/SearchRequestRelationCheck.class
And to deploy it, place it in:
<jira-install>/atlassian-jira/WEB-INF/classes/com/atlassian/jira/appconsistency/integrity/check/SearchRequestRelationCheck.class
The restart JIRA.