Apparently full domain means a domain that has been registered, eg example.com
Then subdomains such as beta.example.com would be counted separately.
As for as "web root", perhaps you mean are talking about the document root? Wether or not it is a domain or subdomain, as long as it is "fully hosted" it will have a document root, which will be located in the home directory of an FTP or shell user. A user can have more than one document root directory in his home directory. Domains/subdomain may even have the same document root (ie example.dreamhosters.com and example.com both have /home/nobody/example.com as the document root).
The subdomain max is per plan, not per domain, and you can also expand the number of domains or subdomains by adding booster packs.
You can add Jabber addresses to any fully hosted domain or subdomain.
I'm not sure about the PHP 5 DreamHost provides, but you can certainly compiled your own with support for those modules.
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