Add capability to filter queries

This change adds a `query-filters` property to the codeql-config file.

This property is an array of `exclude`/`include` entries for a query
suite. These filters are appended to the generated query suite files
and used to filter queries after they are selected.

A related change is that now, all pack references are run in a single
query suite, which has the query filters appended to them.

Author: aeisenberg