Moving to OT > Soft Dev
This is a Tomcat behavior, it uncompressed the WAR and then builds it to the work directory as it runs. Redeploying a new WAR file should trigger Tomcat to see the updated Timestamp and reuncompress it.
Otherwise if you absolutely want to remove that dir, you’ll need to do it manually. It’s not controlled by MYEclipse.
I would point out that deploying in exploded format will give you the behavior you want and your dir will stay updated with your project in real time.