A package is a folder (in 'src', in Eclipse) that Java understand, so that's one way to organize code. https://docs.oracle.com/javase/tutorial/java/package/index.html explains packages (if you don't know that site, its tutorial is very accessible, recommended reading material for learning Java).
EDIT: To make a package in the project explorer, RMB on 'src' in a Java project -> New -> Package. Add Java files by RMB on a package -> New -> Java file. Drag/drop of Java files to other packages starts a refactor to move the Java file, and fix all its references (in the opened projects).
At a possibly much larger scale, Eclipse has a plugin system that you can use. In fact, that's how they built entire Eclipse. A plugin is its unit. It's a piece of functionality, coded in Java, and (typically) stored in a Jar file. It offers some services for other plugins, and uses services of other plugins. This provide / use relation creates a dependency tree. Plugins are otherwise self-contained. A piece of software like Equinox manages the plugins and its dependencies. Equinox also connects service providers with service users. An editor for a language could be a plugin.