From mboxrd@z Thu Jan  1 00:00:00 1970
From: Jambunathan K <kjambunathan@gmail.com>
Subject: Re: Cygwin (org-open-file (org-odt-export-to-odt nil s v) 'system)
 opens odt as zip
Date: Sat, 30 Nov 2013 21:32:12 +0530
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Ignore my earlier suggestion.

> (if (eq system-type 'cygwin)
> (add-hook 'org-mode-hook
> '(lambda ()
> (delete '("\\.x?html?\\'" . default) org-file-apps)
> (add-to-list 'org-file-apps '("\\.x?html?\\'" . "cygstart %s"))
> (delete '("\\.pdf\\'" . default) org-file-apps)
> (add-to-list 'org-file-apps '("\\.pdf\\'" . "cygstart %s"))
> (delete '("\\.odt\\'" . default) org-file-apps)
> (add-to-list 'org-file-apps '("\\.odt\\'" . "cygstart %s")))))

You can also remove the above settings.

----------------------------------------------------------------

Use the following setting instead.

`org-default-apps' uses the value of `org-file-apps-defaults-gnu' for
cygwin as well.  You just need to remove the mailcap entry in that
variable and replace it with "cygstart" as below.

    (eval-after-load 'org
      '(when (eq system-type 'gnu/linux)
         (setcdr (assq 'system org-file-apps-defaults-gnu ) "cygstart %s")
         (setcdr (assq t org-file-apps-defaults-gnu ) "cygstart %s")))

----------------------------------------------------------------
         
As you rightly suggest, `org-default-apps' doesn't handle `system-type'
value of 'cygwin.