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I cant reproduce this 100%, but it happened to me 4-5 times. The best steps I have are here:
1. Create maven project, add hibernate-jpamodelgen dependency and maven-processor-plugin
2. Set project's maven annotation processing strategy to experimental
3. Let the project update
ASSERT: target/generated-sources/apt was added to build path
4. delete maven-processor-plugin
5. change project's maven annotation processing strategy to JDT, update project
FAIL (sometimes..): build path contains both target/generated-sources/apt and target/generated-sources/annotations

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I cant reproduce this 100%, but it happened to me 4-5 times. The best steps I have are here: 1. Create maven project, add hibernate-jpamodelgen dependency and maven-processor-plugin 2. Set project's maven annotation processing strategy to experimental 3. Let the project update ASSERT: target/generated-sources/apt was added to build path 4. delete maven-processor-plugin 5. change project's maven annotation processing strategy to JDT, update project FAIL (sometimes..): build path contains both target/generated-sources/apt and target/generated-sources/annotations

m2e-apt sometimes doesnt delete old build path resulting in having two (or more) same classes in build path. See attached screenshot.

is blocked by

JBIDE-21651 Create and use Mars.2 RC4 target platform