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Build 2.1RC1 + latest jdtcore 1. Create Java project (prj=src=bin) 2. Edit .classpath: <?xml version="1.0" encoding="UTF-8"?> <classpath> <classpathentry kind="src" output="bin2" path="src1"/> <classpathentry kind="src" path="src2"/> <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> <classpathentry kind="output" path="bin"/> </classpath> 3. Save .classpath Observe: You get 2 'Missing required source folder' markers (OK) but you also get a 'Cannot nest output folder 'Test/bin2' inside output folder 'Test' (WRONG)
Looks like this bug was introduced after RC1.
The set classpath operation was incorrectly causing full validation of classpath, even though it had verified it successfully already upfront. Fixed in latest.
Verified.