When the following two lines are used in concert, genshi exits with "OSError: [Errno 13] Permission denied: '/common'"
lookup = TemplateLookup(directories=[fldr], default_filters=['unicode', 'h'], module_directory='/tmp/mako_modules')
<%include file="../../common/ficfan_common.css.incl" />
I've tracked the problem down to line 210 of Template.init() which naively joins module_directory and self.uri.
The solution I see being most feasible is to extend the policy embodied in lines 207-208 (if u == '/', strip it) by treating self.uri as relative to the current template's path.
In my example, that would resolve to "/tmp/mako_modules/common/ficfan_common.css.incl" rather than "/common/ficfan_common.css.incl".