These are all great comments/bug reports.
In order ...
1. You need to customize the context bar yourself and I think this makes sense. Because as a default I think treating an OpenACS site-with-subsites as something of an integrated whole is correct. We might want to parameterize the toolkit so you can install it in a "each subsite is its own world" mode.
2. Making general comments subsite aware should be easy, and it is possible Daveb has done so in his improved version which is in contrib. This will eventually replace the existing general comments package but he needs to fix the gawdawful attachments package rewrite first.
3. Notifications is probably fairly easy to fix.
4. Yes, it would be good to customize subsite group names automatically.
5. Links to global admin doc and similar directories should probably be generated with a fully rooted URL rather than short-handed the way they are.
I don't have time to work on any of these issues myself at the moment, but am available to answer questions by e-mail...
