The third option would be to embed the RAR in your app, but I didn't understand your comment about why that would require extensive app refactoring. In theory, the app shouldn't change, just the config...
See the IBM Knowledge Center topic http://www-01.ibm.com/support/knowledgecenter/SSEQTP_8.5.5/com.ibm.websphere.wlp.doc/ae/twlp_jca_config_resadapters.html?lang=en for details on configuring a connection factory for use with an embedded resource adapter.
For the standalone resource adapter, I assume you had something like this in server.xml:
<connectionFactory jndiName="eis/NAME" type="javax.resource.cci.ConnectionFactory">
<properties.rarName dataStoreName="name" hostName="otherName"/>
</connectionFactory>
<resourceAdapter id="rarName" location="rarName.rar"/>
when you embed the rar in the ear, as you noted, that resourceAdapter node goes away and instead you would use something like this:
<application location="C:/applications/app1.ear"/>
<connectionFactory jndiName="eis/NAME” type='javax.resource.cci.ConnectionFactory’>
<properties.app1.rarName dataStoreName="name" hostName="otherName"/>
</connectionFactory>
Note that for an embedded resource adapter, the properties element must now also include the application name (in this case “app1”) in the name of the element.
As indicated in the Knowledge Center topic, if you wanted to override the default name of the resource adapter, you could instead do:
<application location="C:/applications/app1.ear”>
<resourceAdapter id=“rarName" alias="MyEmbeddedRA"/>
</application>
<connectionFactory jndiName="eis/NAME" type="javax.resource.cci.ConnectionFactory">
<properties.app1.MyEmbeddedRA dataStoreName="name" hostName="otherName"/>
</connectionFactory>