Documentation for JIRA 4.2. Documentation for other versions of JIRA is available too. 
The JIRA API docs are available online. They are most useful for:
- users writing Plugins, Listeners and Services
- users with commercial licenses who wish to modify JIRA
- partners embedding JIRA as a J2EE component
The latest API docs are available at http://docs.atlassian.com/software/jira/docs/api/latest/. The 4.2 docs are available at http://docs.atlassian.com/software/jira/docs/api/4.2/. JDiff reports listing the changes to the JIRA API between releases are available here. For previous versions, substitute the appropriate version in the URL.
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