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The SP software calls a grouping of resources that are meant to be accessed as a unit an "application". This term is used in a precise way and doesn't necessarily refer to something you would actually draw a line around as a "web application", although certainly it can and often does. An application defined to the SP software has a number of important qualities..
Any two resources protected by the same physical SP software (or a cluster) can be aggregated into an application. They don't have to live in the same directory or even the same virtual host. Of course, it's common for that to be the case, and generally a good idea, for obvious reasons. But it's not a technical limitation.
The meat of the software configuration is divided across two sections of the shibboleth2.xml file: the <RequestMapper> and the <ApplicationDefaults> elements. In the case of Apache, the former is generally omitted in favor of Apache-specific commands.
1. User Accesses Protected Resource
2. SP Determines IdP and Issues Authentication Request
3. User Authenticates to the IdP
4. IdP Issues Response to SP
5. Back to the SP
6. Back to the Protected Resource
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