Hi,
Awesome job I was able to get started quickly and felt right at home. I do have a suggestion and a possible bug.
Suggestion: During the waiting to detect plugin portion of the install it would be nice to see platform specific instructions on where to see the plugin if it started and maybe how to manually start it.
Possible Bug: (Mac OS X El Capitan version: 10.11.1 (15B42)) I get two arduino agent logos in my menubar. I wasn't sure if the plugin had launched and I launched it twice. Launching a third does not add a third agent logo. Pausing the agent on one logo does not affect the other. When launching the debug console one logo just spits out usage and quits the other continuously updates serial info.
Again great job!