I think the problem is in line 32 of the jde-plugins.el. This line:
(defcustom jde-plugins-directory (expand-file-name "plugins" (jde-root))
should be:
(defcustom jde-plugins-directory (jde-cygpath (expand-file-name
"plugins" (jde-root)))
This is why the classpath for your plugins all start with
"/usr/share/emacs/site-lisp/jde/java/lib".
However, I don't think it probably ends there, since I'm not sure what the
effect of
having just expand-file-name in other functions such as
jde-pi-get-plugin-dir(plugin) and
jde-pi-load-plugin(plugin) would have on loading beanshell. Those calls to
expand-file-name
should likely also be wrapped in jde-cygpath.
Sorry, I've not used cygwin emacs for years to provide a more modern
first-hand experience
for what all is needed.
-jeffrey
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