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The documented way to configure pterm is by using command-line arguments and/or X resources.
However, pterm also currently takes notice of PuTTY saved sessions in ~/.putty, including Default Settings, and responds to the -load command-line option. Since 0.58, the saved sessions have also been visible on the Change Settings dialog.
This semi-support is more or less by accident. It's not clear that it's the right thing to do, it may be buggy or broken in various regards, and it may go away in future.
We should either support this properly and document it, or remove it.
Audit trail for this semi-bug.