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.
One of the diffs look confusing but:
Previously parameter {2,3} where flagged, now parameter {1,2} are flagged.
Note that for command injection, the SystemCommandExecution is flagged
despite the test file claiming otherwise.
