Is there a recommended pattern in zopeproject for including zcml files.
I can see hacking/modifying site.zcml - is this the recommended way?
Is it simply best to follow the older site.zcml pattern from the mkzopeinstance days?

No. Consider src/<yourpackage> to be a complete and exhaustive definition for your application. This should include all dependencies. In particular, this should include loading all dependencies' configuration. So if your application inherently depends on some other package's configuration, you should load it in src/<yourpackage>/configure.zcml.

You may obviously modify site.zcml. In fact, it's not a "hack" to do so. site.zcml should contain all the things that are specific to the deployment, like the bootstrap admin principal or the security policy (which sometimes may also be application-specific, depends).

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