then the simplest thing for me to do is to pick an app server and write to it specifically
Obscurities aside, all of the application servers, including WebSphere 6, support standard J2EE applications and packaging.
So personally I would certainly target that standard.
Then you need to test it on each of the major application servers and add footnotes where needed as to minor tailoring that may be required on individual platforms.
You might have different install scripts that vary on the different platforms.
That is what major vendor such as Plumtree and Callidus do. They certainly do not have different distributions for the different J2EE Application Servers.
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