So the line that is blowing up is this one:
https://github.com/rubygems/rubygems/blob/v2.4.8/lib/rubygems/specification.rb#L2716

I was able to run the same code in irb on the server like so:

./java -jar jruby-complete-1.7.24.jar -e 'load "META-INF/jruby.home/bin/jirb"'
irb(main):001:0> File.stat("/opt/ibm/WEX/AppBuilder/wlp/usr/servers/AppBuilder/apps/AppBuilder/javascripts/.gitignore").mode & 0444 == 0444
=> true

and it works fine. Any ideas on how I can reproduce this without needing a full warbled rails application?

@atambo This problem is not on windows and unfortunately those issue(s) never touched anything outside of windows. I wonder if jnr-posix native is really loading? -Xnative.verbose=true should tell you if it loaded or something fell back to non-native mode. Even so if this is happening non-native it seems we have an issue retrieving the mode properly.

When I run:

./java -Djruby.native.verbose=true -jar jruby-complete-1.7.24.jar -e 'load "META-INF/jruby.home/bin/jirb"'

I get:

Successfully loaded native POSIX impl.

So it looks like the native stuff is loading. I'm still not able to reproduce the issue outside of a warbled application :(. Let me try inside of the warbled application.

I haven't been able to reproduce this problem after I fixed some other unrelated issues...I'm going to close this for now.

For posterity, I resolved this issue by removing 'noexec' flag from a tmpdir mount.