A very recent change to the languages/perl6 Makefile appears to have changed the make for perl6.exe (after the make for Parrot itself) to

cd languages/perl6
make perl6.exe
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Also, if the make for Parrot dies under Cygwin with this error,

make: *** [runtime/parrot/include/config.fpmc] Error 53
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the problem is that after libparrot.dll is built in ./blib/lib the loader can't find it when miniparrot.exe starts up. The solution is to copy the dll file to another directory where it can be found...

cp blib/lib/libparrot.dll /usr/local/bin
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and rerun the make; it will run successfully this time. Perl6.exe also needs libparrot.dll to run, so you will need to keep this extra copy of it after you are finished.

Enjoy!