Hi!
 
> Should I be able to mix .php and .jsp files in the same
> directory using mod_webapp, and have apache/tomcat figure
> out who will handle it automatically? Or am I being optimistic?
> Or must I separate them out into different directories so
> that apache will know what to handle locally and what to pass
> on to Tomcat?
 
I think mod_webapp should serve only resources mentioned in web.xml
The other question is if Apache will serve php with its mod_php.
So you should look through your web.xml
 
There is another way. You can implement PHPServlet 
(like CGIServlet or SSIServlet already implemented).
I think it will be greatly appreciated by Tomcat-dev team.

> 
> One other question, does a new WebAppDeploy line need to
> be added to httpd.conf for every new webapp that gets
> added?
> 
 
yes and no, WebAppDeploy line should be added for every new
context (like a folder). But your root context will cover any of them, I think

> Sorry for all the questions, just trying to increase my
> understanding of how it all hangs together.
> 
 
No need to be sorry, isn't this the purpose of this list
to increase our understanding? :))

> Regards and thanks,
> Sam.
> 
> 
Anton



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