As confused as most users, i will try break it down gently my perception of it all.
First, you should start by a nicely done history and time line presentation i found, by Matthew Williamson.
Arduino LLC was founded by Massimo Banzi, David Cuartielles, David Mellis, Tom Igoe and Gianluca Martino in 2009.
Considering Arduino idea started around 2005, a lot of these guys had been working togethers since.
The other party is Smart Projects, founded by Gianluca Martino in 2004, which has always been one of the major manufacturers of Arduino Boards.
A rift started ( you can check the full breakdown in the series of articles on Hackaday) and Smart Projects changed their name to Arduino SRL in November of 2014. A new site was started ( arduino.org) and the Clash of IDE's started, confusing a lot of people in the process.
Warnings on some boards started to appear with version 1.6.1 that "Added warning for uncertified boards" ( apparently some USB Vendor ID's from boards manufactured by the "ORG" camp . And this is confusing for the average user.
arduino.cc's version 1.6.3 is the official version, but arduino.org released a few versions with higher numbers to confuse the matter ( 1.7.0 and so on). This version already supports their new Arduino Zero Pro already on sale, while the official team's shop still has it as "Coming soon".
It is sad to see greed, egos and what-not brought to the forefront of public attention, specially regarding a product that is supposed to epitomize the Open Source Community's strength.
Anyone out there surely feels that Arduino is the original idea, perpetuated by the hard work of what is now a massive team. But above all, Arduino is but the massive community that made it what it is today !
All in all... Facepalm !
* Id advise everyone to have a scroll down the hardware index page at arduino.cc and scroll down for some of original boards, etc