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No, I didn't use any fork, but used the master branch of this repository which is version 2.1:
https://github.com/geany/geany/blob/master/meson.build#L3
The problem disappeared after I switched back to 2.0 and added following to my ~/.ssh/config:
Host *
...
ServerAliveCountMax 5
ServerAliveInterval 15
TCPKeepAlive yes
I've been now heavily using it and while there was a small freeze from time to time, no crashes or anything which caused Geany to become unresponsive or lose all its data as before.
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