Your good it's all new .
OR does the IDE check the url each time it starts up for latest additions to the arduino.esp8266.com ...JSON file?
I believe it does updates automatically. You can see by clicking on lower left link in preferences ,takes you to the packages and look through to versions .
I have not deleted anything before downloading . All the existing files would be overwritten I suppose but anything you have added would be left . Just try it and if not successful, go in to where Arduino1.6.x is saved and delete the lot , go into your sketchbook file too and delete "libraries " and download the IDE again.
You can choose where to save the downloaded file if you want . Using linux I put in /opt so I can get to it easily and put any new libraries in there too and don't put a "libraries" directory in sketchbook at all, but that may confuse you, so ignore this paragraph perhaps.