Wildfly 9 final loses track of annotated rest endpoints when rest endpoints added for an arquillian index and jandex index in place

I've been testing Wildfly 9 since CR1. In our test suite, we leverage an arquillian build that takes our build's WAR, and adds some extra classes directly. Some of these classes are rest APIs. I found that after upgrading this branch between CR2 and Final, the REST endpoints placed directly in the WAR file do not function. Most of my REST endpoints go into JARs which go into the WAR, those all work fine.

I'll see if I can create a very simple test case that reproduces this issue.

The error output is generally along the lines of

11:35:35,658 WARN  [com.mycompany.ExceptionConverters] (default task-14) Returning an exception back to the client on failure, : javax.ws.rs.NotFoundException: Could not find resource for full path: http://127.0.0.1:8082/rest/i-test-status