Fix handling of -Astubs=checker.jar/

[wmdietl]

Handling of -Astubs=checker.jar/ doesn't seem to correctly handle stub files that are with the checker or in the root directory.
8d0b965 fixed handling for stub files with the checker.
For stub files in the root directory, one currently has to pass -Astubs=checker.jar//file.astub (note the two //). This isn't documented.
Investigate what the best solution for handling this flag is.

[wmdietl]

Also make sure that the @StubFiles({"junit-assertions.astub"}) (

checker-framework/checker/src/main/java/org/checkerframework/checker/nullness/NullnessChecker.java

Line 57 in 666705f

@StubFiles({"junit-assertions.astub"})

) loads the correct stub file - there are two files with that name in the repo. Should both be loaded?