WPI: isSubtype crash related to type variables

[kelloggm]

I've observed this problem on two different projects. There is an example on this branch (you can observe the failure by running ./gradlew ainferNullnessAjavaTest). Sorry the test isn't completely minimized, but hopefully it should be minimized enough to get the idea.

The symptom of the problem is a crash in QualifierHierarchy:

      :-1: other: error: QualifierHierarchy: missing annotation in hierarchy @org.checkerframework.checker.nullness.qual.NonNull. found: @org.checkerframework.checker.initialization.qual.Initialized

with the following stacktrace:

        at org.checkerframework.javacutil.BugInCF.<init>(BugInCF.java:34)
        at org.checkerframework.framework.type.QualifierHierarchy.isSubtype(QualifierHierarchy.java:140)
        at org.checkerframework.common.wholeprograminference.WholeProgramInferenceImplementation.updateAnnotationSet(WholeProgramInferenceImplementation.java:876)
...

Based on this stacktrace, I suspect that there is something wrong with the fix we merged a few days ago in #5618. @smillst if you have a chance to look at this this morning, I'd appreciate it. I'll take a look in a few hours, but I'm busy until about 2pm eastern time.