gjt3,
In the newer versions of MyEclipse, your projects’s final archive can be customized using the Deployment Assembly page. Right click on the project > Properties > MyEclipse > Deployment Assembly. You can remove the files that you do not want to be deployed with the project from this page.
Please refer to this tutorial about Deployment Assembly for more details :
https://www.genuitec.com/docs/servers/deployment-assembly/
If you are still seeing issues, then please share with us more details about how you are referencing the IBM runtime files in your project along with a screenshot of the Deployment Assembly page to help us get a visual.
–Swapna
MyEclipse Support