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I've made a firewall exception, opened ports 22 through 443 to the correct internal IP (I think), and am able to log in using my external IP, but it's like I have very limited view access to almost any commands or files.

/home only has .bash_profile

/bin only has about 20 commands, half of which start with cyg. but I'm at a loss as to why all my directories are empty. Any one point me in the right direction?

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Not a firewall problem, for some reason you are connecting to some wrong account/cygwin configuration (or perhaps to the wrong machine?). – vonbrand Apr 15 '13 at 3:05
@vonbrand: It's definitely my machine. I receive Access denied messages until I enter my correct credentials. The Cygwin install is a day old with all packages selected for install. I haven't customized Cygwin or anything that I can think of that would cause this. – user37185 Apr 15 '13 at 3:21
Perhaps you're SSHing into a chroot environment? – depquid Apr 25 '13 at 13:45
@user37182 : if you haven't customized Cygwin at all you miss a step. You have at least to setup Cygwin SSH Server. Probabily the problem is this. – DavAlPi May 25 '13 at 11:43

This can be normal if your CygWin installation is brand new and you do not install any packages using CygWin setup.exe install program.

The CygWin setup.exe install a bare minimum, if you dont select any package in the apropriate step. Non even a vi is installed by default.

In Cygwing your home is empty in a fresh installation.

Try this: open Cygwin Terminal localy on the Windows box and check your home and /bin folder: if they are the same that you see connectiong from remote then you have to install all is missing using CygWin setup.exe

Check CygWin docs: http://cygwin.com/cygwin-ug-net/using.html

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