I work on a fairly large code base (only 4MBytes code but ~50Mb libraries). Our code mostly extends classes from a commercial package from ATG, this leads to our code having lots of code paths going in and out of the framework classes and libs.
To get meaningful results, I indexed most of the jars we rely upon excluding the jre jars most of the anwsers I want are linked to ancestry and call graphs (One I want to write is the call graph of a method within the boundaries of a type hierarchy) so having the ancestors of my classes fully indexed is important for me

I then tried running a few queries from the default metrics. Seeing the queries were taking some time to run (which is fine considering the sheer number of elements to work with), I tried running a junit test to continue a debug I am working on => the semmle query blocked it

Is this normal/expected ? can/will it be changed ?
I'd rather be able to use my workspace while the queries are running...