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Yes, I am using the emacs-X11 and yes, I started it (after starting the X server to get multiwindowed mode) with ">emacs&" at the cygwin command. Emacs-X11 comes up fine, looking good. Then I do "M-x shell" to get a shell environment inside of Emacs. But what comes up is not bash. I'm not sure what it is, but it sees no cygwin apps: It doesn't know what "ls" or "which diff" or any other GNU/cygwin stuff is. I assume it is the DOS shell. Oddly, if I start emacs-X11 inside the windowed mode (startx) and do emacs shell mode, it does see bash and the rest of the GNU/cygwin apps.
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