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The configuration of the remote programming functionality has two separate parts: the tools configuration (remote connection tools, shells, and rsync parameters) and the servers configuration.
The first part (see Defining a remote connection tool, Defining a shell and Configuring rsync usage) is handled by a pre-installed file in the plug-ins directory called protocols.xml.
The second part (see Defining a remote server and Defining a remote path translation), when configured via the user interface (see Setup the remote servers), will create a remote.xml file in the user's gps directory. System-wide servers can be also installed.