While searching for the reason why net/ssh didn't pick up my keys from my home folder, I noticed that Dir.home is pointing to the path defined in the LOGDIR evn variable.

In org.jruby.Rubydir.getHomeDirectoryPath() the order is

1. LOGDIR
2. HOME
3. user.home

According to JRUBY-6295 in Jira it should be

1. HOME
2. user.home
3. LOGDIR

(which makes much more sense).