No there is no guarantee ordering of entries is honored.
Could you clarify - it's not guaranteed to be supported in future or it's not supported now? And was your answer relevant to all 3 my questions?
Note: I do consider it as a bug. Placing jar at the beginning of classpath to override some classes is not that unusual approach. Java supports it and if I'm not mistaken Java EE specification doesn't forbid it.
Can we define order programmatically? (even if it will require jboss source code patching)
After deep study of JBoss source code we discovered that order of <resource-root> entries from jboss-deployment-structure.xml <resources> tag entry is considered indeed. Not sure about Class-Path entry in manifest though.