Need security first
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I like the idea in general. Need to first add a major layer of security as a first step.
With a level of security what do you think about? If a user want, he can change the SSH username and password on the board and configure the remote deployer with custom username and password or with an SSH Key (I added this thing in my last review of proposal)
If we can simply use ssh, then a simple shell script on top of 'scp myscript.js email@example.com:/var/lib/cloud9/autorun/' will actually already do the trick. I was thinking we needed to do something to secure the BoneScript web server and that it would be handling the connection. At one point, I was building up my testbanch to do BoneScript RPC testing: https://github.com/jadonk/bonescript/blob/master/test/TODO/remote_bonetest.js. With the PRC, you can simply do "b.writeTextFile("/var/lib/cloud9/autorun/myscript.js", MYSCRIPT_JS);".