[joosters]

Cygwin does not alter the behaviour of existing programs. It is a DLL that can be compiled into new programs to provide lots of POSIX/Linux compatibility. It also comes shipped with lots of pre-compiled Linux binaries of common tools.

If you run your pre-existing JRE, its behaviour won't change. If you run a JRE compiled with cygwin (I've no idea if they provide one or not) then it will have UNIX-style path support.

[yareally]

Don't believe there is such a JRE. I mostly handle paths like I would normally on windows and they work ok on the JVM:

"c:/whatever/another_dir/some.file"

There's also cygpath to convert between Windows/Unix style paths: http://cygwin-lite.sourceforge.net/html/cygpath.html