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In practice, locations of certificates are constrained somewhat.
There are potentially four pieces of data to install or make accessible for each server application.
1. The host private key
2. The host certificate
3. The OrganizationSSL (or IntranetSSL) Intermediate Root Certificate
4. An appropriate Certificate Authority Root Certificate
Of those, 2 (the host certificate) is the one you will always need to install or update. If you generated a new 1 private key, you will need to ensure it is correctly updated to match each certificate you install or update. In general 3 (intermediate certificate) will have been appropriately installed, unless you are setting up a brand-new server.
And 4 (CA root certificate) isn't actually required by most server applications. A CA root certificate is really only meaningful to the clients if it is obtained from a source different from the server presenting a certificate allegedly signed by that authority. Nonetheless, many servers are set up with CA root certificates available, although most client and server software will not actually have any reason to access that particular certificate from that source.
-- AdrianPepper - 23 Feb 2011
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