I�m working on my project both at home and at work and my girlfriend is also working on it remotely.(We use dropbox to store the project folder).
At the moment, the usual popup that alerts about the missing plugins has been enough, but in the future I fear I�ll loose track of what custom plugins/behaviors are being used(also, some of them may become dated).
I think some form of "Store plugins/behaviors in the project folder" option could be useful, so instead of depending on the plugins locally on your Construct folder you could have them inside your own project folder, making working on teams/updating the plugins easier. ;]