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Rather than newest last write time of all dlls loaded, use the forking process' windows pid and windows thread id as directory name to create the forkable hardlinks into. While this may create hardlinks more often, it does avoid conflicts between dlls not having the newest last write time.
THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. Cygwin documentation is available on the net at https://cygwin.com You might especially be interested in https://cygwin.com/faq/faq.html#faq.programming.building-cygwin