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Wow -- this is the longest question I've ever gotten!
Nagios is a very flexible product that can undoubtedly accomplish what you want to do. It is very capable of accommodating custom-written plugins of the sort you describe. For some more information, take a look at an article I wrote about Nagios a few months ago.
Regarding your two specific questions, here's what I would say:
You can use Nagios to drive custom plugins (there are also a large number of community-contributed plugins that might serve your purpose). Nagios is architected to allow plugins; the plugins are installed on the remote machine and executed via the central Nagios server. The plugins can pretty much do anything you choose, so you should be able to accomplish what you want.
Regarding returning the info via XML and having Nagios store it in a separate database, I am not sure if the native Nagios protocol and server can implement that. You would need to take a detailed look at the documentation to see what it is capable of. If it can't be done natively, you have a couple of choices:
1. Modify the Nagios source code to enable XML and use of another database. While this is an option, I wouldn't recommend it, as it's difficult to manage unusual source forks in open source projects.
2. Design your plugins to return XML data to another server that you write, which places the data into your desired storage mechanism. In this way you take advantage of Nagios and extend it through plugin extension (which it's designed for) rather than modifying the basic architecture.
Good luck!
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