Current setup:
MainProject which is a Library Project
BranchProject which is a new projects and has MainPr
Most of the time it happens when specific source folder are not added in build path Sources tab.
Right-click on the Project in the Package-Explorer, click Build Path -> Configure Build Path -> Source Tab
Add the source folder if your project source folder is not there. Select Add folder -> select your project source folder specifically. Eg: project_name/src . Then Apply it and restart server.
The problem is that the class file is preferred over the java (by default), here is how you can change that for Eclipse (tested on NEON 2):
Skyler's answer from this post worked for me: Opening source code from debug view edits .class after Android R18 update
Here is a summary: The fix is to right click the Project name in the debug view, and select "Edit Source Lookup..." from the menu. From there, remove the Default lookup path. After that, manually add the associated projects (not jars) that your project references. This is done by clicking Add, selecting Java Project, then checking the appropriate projects.