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The javadoc on IJavaElementDelta.getCompilationUnitAST says that it returns "the compilation unit AST created by the last reconcile operation", which seems to imply that it has been processed by both the main jdt compiler and any annotation processors. But when I call getProblems() on that AST I only get diagnostics from the base compiler (syntax errors, bad types, etc) and not any that were generated by an annotation processor, even though those do show up in the source view.
APT uses ReconcileContext#putProblems(...) to report problems. This specifies that these problems are reported to the problem requestor, not added to the AST. Also CompilationUnit#getProblems() specifies that the problems are the one created by the compiler (not by a compiler participant). Works as designed.