Composite applications can work fine; sometimes, as you have discovered,  
components have per-process configuration instead of per-WSGI-application 
configuration and won't cooperate properly.

Obviously you have to compose at the WSGI layer to host something unrelated 
like Trac alongside your Pyramid application. If the second application has 
to integrate with your application, like a reusable login form, WSGI 
composition is a pain and Pyramid config.include() will be better.

You should have one entry point per application. With the paster composite 
middleware the configuration looks something like

[composite:urlmap]
use = egg:Paste#urlmap
/foo = egg:fooapp:foo
/ = egg:fooapp:bar

If those are both Pyramid applications then you will eventually have two 
unrelated Configurator()s that create two separate WSGI applications.

Personally I try to avoid WSGI whenever possible. I prefer to use it only as 
a gateway interface to a web server, not as an ill-fitting tool for 
application composition.

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