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Good questions. I'll try to answer them.
1. When using the AgileTrack server, you can set up a centralized server that all clients communicate with using either an HTTP based protocol, or a direct JSON-RPC protocol.
2. There is no web interface currently. A web interface is in development, but it has stalled currently due to lack of time.
3. Processes can be customized in terms of a state flow for different issue types. There is no state configuration UI in the current release. Contact me for details in customizing states.
4. Process automation is accomplished by specifying the relationship between states on a record. Each state can be a assigned a list of available next states. When the state flow option is turned on, a user will only be presented with a list of available next states when making changes.
Hope that helps.
Thanks Adam.