This adds Alert annotations for alerts that seem intentional by the test
but has not been annotated with 'NOT OK', or the comment was in the wrong
place.
In a few cases I included 'Source' expectations to make it easier to see
what happened. Other 'Source' expectations will be added in bulk a later
commit.
The `queries.xml` file defines which extractor the `codeql test` runner will use
to extract databases for the tests. In the future one will be able to write this
information in `qlpack.yml`, but we can't do that immediately because the
_existing_ CodeQL tooling would refuse to parse a `qlpack.yml` that has the new
field in it.
Adding a queries.xml file means that the normalization of file names in the test
output changes even with the old QLTest, so there are a number of consequential
updates of expected output files.
