As far as I can see, this is neither an Ubuntu nor an XFig issue, but
some misunderstanding how X resources work at all.

There is one global app-defaults directory, that is read by the X
server.  In Ubuntu this is usually /etc/X11/app-defauts.  As far as I
can see, you cannot use a different directory for a single program, so
/usr/local/share/X11/app-defaults/Fig will never work.

You may want to have a look on http://www.tldp.org/HOWTO/XWindow-User-
HOWTO/moreconfig.html#xresources which explains most of this a little
wider.

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https://bugs.launchpad.net/bugs/1635944

Title:
  XFig only looks for system-wide app-defaults

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