Nelson asked:

3. Is there a good mediawiki book that I can find examples for basic (e.g.

creating a page, edit a page, setting directory & files permissions, how to incorporate an extension...) operations? Of course if there is a comprehensive list of mediawiki commands (I mean .php files) and their usages will be even better.

I'm not sure of the quality, but there is at least one MediaWiki book that you can get on Amazon:

MediaWiki Administrators' Tutorial Guide: Install, manage, and customize your MediaWiki installation (Paperback - Mar 22, 2007) by Mizanur, Rahman