Cygwin symbolic links are nothing more than a file that talks about a link. Here, what you will find when you look at the contents of one of the Windows cmd prompts:
C:\>type c:\cygwin\bin\emacs !<symlink> ■/ etc / alternatives / emacs C:\>
AFAIK, NTFS Windows connection points are something completely different. I would expect that since they run at the file system level, cygwin does not see anything else in them from any other file / directory.
Having said that, I will also say that I did not play with NTFS junction points, therefore YMMV.
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