RE: serving WO app through a proxy server

> How do I tell my app to look for apps using /BAR/cgi-bin/WebObjects as a
> prefix?

Modify you http adaptor configuration. In case you're running apache web
server, 
change WebObjectsAlias directive in apache.conf file which is usually
located in $NEXT_ROOT/Library/WebObjects/Adaptors/Apache/.

# You can change the 'cgi-bin' part of WebObjectsAlias to whatever you
# prefer (such as Apps), but the 'WebObjects' part is required.
#WebObjectsAlias /cgi-bin/WebObjects
WebObjectsAlias /BAR/cgi-bin/WebObjects

hope this helps,
--
 marius
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