The easiest way to upgrade to the latest version of ImageJ is to use the Help>Update ImageJ command, available in version 1.41 or later. Use the ImageJ Updater plugin to upgrade earlier versions.
The Update ImageJ command downloads the latest jar file (ij.jar) from rsb.info.nih.gov/ij/upgrade/ij.jar. The Java source code is available at rsb.info.nih.gov/ij/download/src/. It downloads the "daily build" jar file from rsb.info.nih.gov/ij/ij.jar. The "daily build" source is at rsb.info.nih.gov/ij/source.