Patching EAP 6.2 breaks classpath jar files

Using the JBoss CLI command 'patch apply .../eap-6.2.2.zip' breaks some of the module jars (the files become invalid ZIP-archives).

This is apparently done as a way to mark the modules off-limits for the container, while still allowing roll-back if necessary.
See https://access.redhat.com/site/discussions/726623

Unfortunately, Eclipse includes these jars in the JBossTools-defined classpath. When scanned, these will be found corrupt, and the project classpath marked as broken.

On my installation, the first few files to trigger this problem are:

• modules/system/layers/base/javax/el/api/main/jboss-el-api_2.2_spec-1.0.2.Final-redhat-1.jar
• modules/system/layers/base/javax/el/api/main/jboss-el-api_2.2_spec-1.0.2.Final-redhat-1.jar

I guess it might be possible to adjust the server definition's Default Classpath Entries in Eclipse preferences. But I decided to just copy the original EAP 6.2 files on top of the runtime and get on with work...