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This section is incomplete. Please share your solutions.
Cygwin’s ssh works only with a Cygwin version of
Emacs. To check for compatibility: type M-x eshell, and
start ssh test.host. Incompatibilities trigger this message:
Pseudo-terminal will not be allocated because stdin is not a terminal.
Some older versions of Cygwin’s ssh work with the
sshx access method. Consult Cygwin’s FAQ at
http://cygwin.com/faq/ for details.
When using the scpx access method, Emacs may call
scp with Windows file naming, such as c:/foo. But
the version of scp that is installed with Cygwin does not
know about Windows file naming, which causes it to incorrectly look
for a host named c.
A workaround: write a wrapper script for scp to convert Windows file names to Cygwin file names.
When using the ssh-agent on Windows for password-less
interaction, ssh methods depend on the environment variable
SSH_AUTH_SOCK. But this variable is not set when
Emacs is started from a Desktop shortcut and
authentication fails.
One workaround is to use a Windows based SSH Agent, such as Pageant. It is part of the Putty Suite of tools.
The fallback is to start Emacs from a shell.