Plugins are written to enhance JIRA's functionality. There are many tutorials available and for me, the simplest one being adding your own menu item.
There is also a simple tutorial I have written which you might find helpful.
Let us know if you need any help.
To answer your question where to store java code?
When you create a jira plugin module, you enter the class name and package name. You will find these .java files created under your plugins /src folder where you can write your own implementation.
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