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Perhaps the best fix here is to use Maven War overlays (or the Gradle equiv) to build a directly-deployable artifact? That has always worked much better for me than pushing "naked" JAR files in and out of web apps.
Just noticed that based on the fcrepo-syn install tasks in its playbook we never actually copy the jar into the fcrepo webapp.
Just tried to do a test against a running claw-playbook.
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