First off, I don't have any personal experience with plotly, but I've used other data services, so the experience may carry over.
cipri92:
First, why doesn't the program contain login credential lines? Shouldn't I be the only one with the streamed info?
It doesn't include them for security reasons. Instead of login credentials, which if intercepted can be used for many different purposes, it includes a unique stream token. That token is tied to your account, and the only thing that it can be used for is to write data to your stream. If it were compromised (by posting code or intercepting the communications) while it could be used to inject false data into the stream, that's all you will be able to do. If the full login credentials were included, besides injecting data into the stream, you would be able to read the past data from the stream, change account settings, etc. A much higher risk.
Second: what's with the Linino? Is that a copy of the original Yun?
That's the old name for the Linux side of the Yun. It is now based solely on OpenWRT. Generally, wherever someone/something makes reference to Linino, you can usually safely pretend it says OpenWRT (or even Linux.)
Third: what's with the json file?
Good question. It's hard to say without seeing the file, or the corresponding Linux code that references it.
Fourth: what's with the uncommenting the 3 lines from the first part of the code?
Uncommenting those lines will cause the Linux side to run the run_plotly.sh script. It's impossible to say what that accomplishes without seeing that script file (and whatever other files it references.)
And last, for now: what's with the timezones?
The plotly servers probably store all data in a common time reference, like UTC. You specify the time zone so that when samples are sent to plotly, the server will know how to adjust the sample's timestamp to get it to the common time reference. That way, you can have sensors all around the world sending in samples, and still be able to correlate the data. (That being said, I don't see where a time stamp is included in the sample -- maybe they took the cheap and easy way in this code and just used millis() instead of a timestamp?)
cipri92:
Now you can move it.
I agree with AWOL, why move it? While there is programming involved, many of the questions you ask seem to be specific to the Yun. I think this is the forum where you will get the best answers. (For example, no other Arduino has the Process class or a process to run under Linux.)