Looks like the queryDsl processor depends on javax.persistence, but doesn’t declare a dependency on it. To work around, you’ll have to manually add it to the annotationProcessor configuration. Consider opening a bug for queryDsl. They should add a dependency on it so it automatically brings it in for processing.
Note that the processor path (used for loading annotation processors and compiler plugins) and the compile classpath (what your code is allowed to link against) are two separate and different things. Dependencies on one are not visible to the other.