Closing as solved by XWIKI-19708: no XWiki pom references the Jakarta Persistence API, it only reaches the WAR as a transitive dependency of hibernate-core (currently javax.persistence-api 2.2 through Hibernate 5.6). It will become jakarta.persistence-api 3.2 with the upgrade to Hibernate 7, so there is no separate work to do.
This is also not tied to the Jakarta EE version (XWIKI-22774): the supported Servlet containers (Tomcat, Jetty) don't provide Jakarta Persistence, so its version is a choice of the WAR.
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