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The function of "public IRemoteConnection getConnection(URI uri)" in the class of RSEConnectionManager doesn't work well when the name of rse connection is different from the name of the host. The function uses the host name gotten from the given uri to query the connection list, this only works when the connection name is the same with the host name. I am not sure what ptp component the class RSEConnectionManager is in, so I just file the bug against the core.
You need to use a URI of the form "rse://host_name/path?connection_name". See bug 287185 for more information. Note that their final implementation seems to be a query that just contains the connection name, not "alias=connection_name".
This would require a change to RSE.