Right. Way I do that (bearing in mind I use Linux here, you could do this with Windows, if you used WinSCP + Putty or something)...

In the terminal, on my desktop, in my application's folder..

mad make # tell MADDE to build my project
scp bin/myapp 192.168.0.5:/home/user/myapp # copy myapp executable to my n900
ssh root@192.168.0.5 # connect to my n900 via SSH, so I have a terminal on there
chmod u+x /home/user/myapp # mark myapp executable
/home/user/myapp

You can also just open the terminal on your n900, and run '/home/user/myapp' manually.

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If you were using Windows, you'd open WinSCP, connect to 192.168.0.5, copy myapp executable to /home/user, mark it executable (by right clicking the n900 copy, and properties, or something - I haven't done this in forever, so I forget how), then use PuTTY to connect to your n900 and run it as above.

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There's probably a million ways to do it - this is mine. Hope this helps.