Today I ran into the problem that symlinks created under cygwin using "ln -s" are not understood by Windows, and of course Windows shortcuts are seen by cygwin as regular files. Happily, this is a (semi-)solved problem. For reference, this is what needs to be done: Add "winsymlinks" to your CYGWIN environment variable. For example, in my .bashrc I have the following: export CYGWIN="nodosfilewarning winsymlinks" This makes cygwin create symlinks differently, in a form that is understood both by it and by Windows.