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I'm trying to run GATK integration tests locally on a custom walker. This was working fine for a few days. This afternoon, inexplicably, one of the integration tests began to fail with a MalformedWalkerArgumentsException, which happened because PluginManager wasnt able to find the walker class anymore. I ignored this for the time being and continued working on a second walker (integration test working fine). However, a few hours later this walker also stopped being resolvable by PluginManager. Neither of those class names changed (although code did).
On the assumption that something was out of sync w/ Intellij, I did 'mvn clean', rebuilt the project in intellij and ended up invalidating caches in intellij. If I pause in PluginManager, I see that reflections.getSubTypesOf(pluginType) doesnt find my walker classes (line 153). When defaultRelfections is created, it does contain the right directory in the classPath, and other walkers besides these 2 (including other custom ones) continue to work. I'm running out of ideas on this. Is this something your devs have seen before? Thanks for any help.