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There are 3 places a deployment plan (partial) can be associated with an ear, and they are used in this order:

1. external plan to be specified during at deployment time
2. ear level geronimo-application.xml
3. module level geronimo|openejb-*.xml

So, anything in an external plan takes precedence over bits in (2) or (3) configuring the same module. Anything in (2) takes precedence over a module level plan. If a module level plan is missing from (1) its looked for in (2),then (3); if missing from (1) and (2), then its looked for in the module (3).

There is no attempt to merge plans from these different locations: e.g. if there's something in (1) for a module, any other plans are ignored.