Unlike the (currently) accepted answer, I argue that placing something under WAS_HOME/classes is a laid-back practice. This directory is often used by IBM to host class / JAR files that are considered "internal" to WAS and related products (for example, certain versions of WebSphere Portal place JAR files in this directory).
In addition, placing elements in WAS_HOME/classes makes the elements available to all applications running on all WAS profiles created from this WAS installation. You cannot change this behavior; that how was designed. This is another reason to conclude that WAS_HOME/classes should be reserved for internal use of WAS.
This argument can be generalized almost anywhere in WAS_HOME : user files (that is, files not provided by the software vendor) should not be located in places controlled by the product installer / uninstaller. The WAS_HOME hierarchy WAS_HOME managed by IBM Installation Manager (or the WAS installer, depending on the version of WAS). I would by no means put any of my files.
Now back to your question. If you must have your property files “free” (that is, not included in any particular EAR), the best thing to do is:
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