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An FTP server on the Amiga side is the way to go if you want to do this via TCP/IP, to smooth this over from your editor experience you'll need to script up something from the client side of course.
Like you could just have a makefile that has a ftp upload target in it, so that a `make all` copies the binary over.
Edit: Okay scratch that.
Just read the Squirt docs, don't do ftp. Just use that, combined with a makefile you can then completely do a complete upload->execute->read results cycle using some makefiles/scripts etc.
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