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If you set a breakpoint in Java code that has been generated by an active annotation the debugger will never stop at that breakpoint, even though the corresponding Java statement is executed. I assume this is because there are not line mappings to Xtend code for that Java line.
The line information is missing because the expressions have no source element. With the new Associator#setPrimarySourceElement the situation has at least somewhat improved since you can now set breakpoints on the signatures of methods/constructors.
This is not limited to active annotations. Many breakpoints in the Java code are not hit. package foo class Foo { def static void main(String[] args) { println(new Foo().getBar()) } def getBar() { "bar" } } Set a breakpoint in the getBar() method in the generated Java code and debug the main method. It doesn't stop.
*** Bug 383441 has been marked as a duplicate of this bug. ***
This was fixed in JDT in Mars.
Requested via bug 522520. -M.