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Currently there doesn't seem to be a way to find out whether a server supports the whole Java EE 5 specification. For example the Tomcat 6 platform claims to support Java EE 5, although it is only a web container and therefore supports only parts of it. This might actually be an issue in the tomcat plugin, maybe it shouldn't claim to support Java EE 5 in the first place. This information is needed at least in the persistence unit wizard to determine whether a default persistence provider is supported.
The workaround for 6.0 is made through introduction of "defaultPersistenceProviderJavaEE5" as tool name for isToolSupported. Each server that provides persistence provider (Java EE 5 or greater) should return true for this tool name. In future there should be an api - something like hasCapability or similar. The EE spec version is not enough to recognize the capabilities of server (I suppose this will be more significant for EE 6).
Already resolved by javaee.specs.support.