Allows us to analyze and then check that certain queries were included
in the analysis and others were not.

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.

Also simplify some computations.

Co-authored-by: Henry Mercer <henrymercer@github.com>

Removes duplicated yaml.

Also add some better typings.

…ueries