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it is possible to have multiple instances of the APEX Listener deployed on the same JEE container. I didn't actually do this with WLS, but I don't know any reason why this should be different on WLS than it would be on other JEE containers.
You should start by preparing the apex.war to have the parameter config.dir set in the web.xml . We chose to let it point to a base directory for all config files having one subdirectory for each deployed instance, so we have to do this only once with every new release that comes in. By the way, this is the first location of the sequence to be checked by the APEX Listener upon startup.
Then you can deploy this war file multiple times giving each instance a different application name/context root. We chose +<apex_dbname>+ as pattern for this, but that's up to you.
Note that you may have to provide the static files ("images") for APEX multiple times as well if you don't have the same APEX version on each instance or if you use different custom files that shall not be the present on each instance or in different versions for at least some instances.
In that case, you'll have to configure your WLS to provide multiple "images-applications" as well. We chose to have one for each instance and use +</i_<dbname>/+ as pattern here. If you used the default image prefix +/i/+ so far, you can reset it using the corresponding script provided in the APEX installation package. I'd recommend to use the script version of the package that corresponds to the APEX version of the instance you want to configure.
That might sound complicated, but actually it's not. It's just a few things to keep in mind before starting and once you've set it up, it's really easy to handle.
Thanks Udo - this was very helpful.