in general, you need to be careful when importing a lot of custom jars as they can easily conflict with some OOTB jars. I would recommend include your jars in the app server classpath as the first option. What is your app server?
don't think so. The first option is standard practice for all app servers (Websphere, shared lib; jboss eap use custom modules, etc). If you need detailed help, create a SR with GCS. Someone can walk you through step-by-step.
But I am curious why you need to import so many jars into pega, the chances are some of your jars will be conflicting with pega. You should also use a unique codeset name so that if something is wrong (you could break some OOTB functionality in the worst case scenario) so that you can delete those jars with certainty. To use your own code set, need to create a DSS:
that is exactly what I suggested. As a side note, you may want to reconsider your design approach how to integrate pega with your java applications. Do they have to be so tightly coupled with pega, considering using REST service to expose some of the features from your applications if possible. I do not know your specific use cases, but want to bring it up and a thought for your team.