Eclipse Build Path Nesting Errors

I wanted to throw in a non-mavenish answer to this thread.

Due to version control and strict directory structure reasons, I was unable to follow Acheron's answer (the best answer) of doing something similar to removing src/ and adding src/main/java and src/test/java to the build path.

I had actually been off-and-on battling this nested build path issue for a couple weeks. The answer to the problem is hinted in the error message:

To enable the nesting exclude 'main/' from 'final/src'

Fix

In your build path, you need to edit your Inclusion and Exclusion Patterns by clicking on Excluded: (None) and then Edit...:

1. Go to the navigator and press right click on the project
2. Build Path
3. Configure Build Path
4. Source (tab)

There you can add main/webapp/WEB-INF/classes as an Exclusion Pattern. Then it should allow you to add main/webapp/WEB-INF/classes to the build path as a separate source folder.

I had the same problem even when I created a fresh project. I was creating the Java project within Eclipse, then mavenize it, then going into java build path properties removing src/ and adding src/main/java and src/test/java. When I run Maven update it used to give nested path error.
Then I finally realized -because I had not seen that entry before- there is a <sourceDirectory>src</sourceDirectory> line in pom file written when I mavenize it. It was resolved after removing it.

Here is a simple solution:

1. Right click the project >> properties >> build path;
2. In Source tab, Select all the source folders;
3. Remove them;
4. Right click on project, Maven >> Update the project.