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Depending on your connection type, when you configure a connection, you supply information on one or two forms:

Service Setup
Contains information such as the server address. This information is stored in your settings file.
Configure Connection
Contains information about your connection protocol (how your computer connects to the server). This information is stored in the appropriate .fcp file.
There is one .fcp file for each connection protocol. Normally, all settings files that use the same connection protocol obtain their connection information from the same .fcp file. The .fcp files are located in the FirstClass FCP folder.