Description of problem: The jboss-tools error that still gets reported during some upgrades is well understood enough that the error could be accounted for in the upgrader. A warning could be logged indicating that the upgrade is being skipped for the jboss cartridge in affected apps. Alternatively, blacklisting can be supported.
This case isn't a product edge case but rather a user's choice to break the upgrades. And it really isn't the right thing to hardcode the user's dir choices into the product.