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Updated Cygwin Build Instructions #645

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@ied206 ied206 commented Jun 17, 2015

Sorry for naughty commit logs. I'm not good at using git yet :(

Updated README.md to include Cygwin Instruction link, and refined README-Cygwin.md.
I found patching Makefile can be broke by different options or Makefile structure's change, so from this commit, it will patch Makefile.in instead of Makefile.

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