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Description
This seems very similar to #1237, which was resolved on the JRuby 1.7 track a while ago.
Symptoms: on a customer Windows server, the C: folder was filled up and the application(s) stopped working correctly. Upon careful examination, we discovered loads of temp files.
The jruby-* subfolders have content that looks like this:
(I treat this as two different issues, just leaving the images here for the sake of completeness. Will follow this up a bit more myself but if anyone has any obvious ideas, please let me know.)
The jffi files turned out to be very simple to reproduce locally:
$ java -jar jruby-complete-9.0.5.0.jar -e "require 'ffi'"
This will create a jffi file in the temp folder (in my case, C:\msys64\tmp).
I also tried downloading jruby-bin-9.0.5.0.zip and running with that. Surprisingly enough, the result is different:
plundberg@DESKTOP-NVMNDAM MSYS /c/jruby-9.0.5.0
$ bin/jruby -v
jruby 9.0.5.0 (2.2.3) 2016-01-26 7bee00d Java HotSpot(TM) 64-Bit Server VM 25.66-b18 on 1.8.0_66-b18 +jit [Windows 10-amd64]
plundberg@DESKTOP-NVMNDAM MSYS /c/jruby-9.0.5.0
$ bin/jruby -e "require 'ffi'"
This does not create any stale temp files whatsoever. 😲
Any clues?

