It took me half a day to figure out, why redeploying a Atmosphere war bundle always fails with a stacktrace. Atmosphere packages, e.g. the jersey into the war archive. This behavior could be changed by setting a JVM environment variable in Glassfish.

In the GF admin console, going to:

Configuration->JVM Settings

switch to the JVM Options tab and add this option:

-Dcom.sun.enterprise.overrideablejavaxpackages
=javax.ws.rs,javax.ws.rs.core,javax.ws.rs.ext

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