Mergeback v2.2.4 refs/heads/releases/v2 into main

Remove TRAP caching feature flag

We had a problem where `waitForProcessing` was not completing before
the node process ends. This is because using `unref` would allow the
node process to end without having the `delay` function complete.

Avoid unref-ing timer while awaiting status upload

This refactoring commit changes databaseRunQueries() to accept a list of
flags instead of separate memory and threads flags.

Clean the npm cache before running install

This refactoring commit changes runQueries() to calculate the set of
indices with non-empty custom queries early. Doing so allows us to check
early on whether there are any custom queries to run.

Set --expect-discarded-cache option

Update default CodeQL bundle version to 2.12.3