Upgrading from OS X 10.8.5 to Yosemite: Potential challenges I have a Macbook Pro with OS X 10.8.5 currently installed. I have the corresponding Xcode as 5.1. Now In order to use Swift we need Xcode 6 and above which is only available for OSX 10.9 or later. 

My question: 

I had to upgrade my OS sooner or later even if I was not using Swift. My concern are:
1).I have lots of softwares installed on my current Macbook. Like I have Anaconda Python Distribution package. Similarly I have R studio , IDLE (Python 3.3) using Homebrew Package Manager etc. When I click on the online upgrade to Yosemite, will I lose all the existing softwares installed on my current OS?. What about other files? 

2). Also in case I don't lose my existing softwares, will the existing softwares stop working especially like Anaconda etc due to some compatibility conflict? 

I think I would have to upgrade to new OS which is Yosemite currently but I am very sceptical if this would make me lose my current set of softwares and files or make them incompatible with others? Some of those softwares installation is really a big pain like installing new Python using Homebrew along with other lib. 

Please advise. 

Thanks
I can't directly answer your specific questions but I advise you to wait before upgrading. Right now version 10.0.1 is out and I still have a couple problems I never had on Mavericks (now imagine all issues you'll have coming from 10.8). 
But as far as I remember from upgrading to Mavericks a year ago, I didn't lose any software or packages nor did I have any problems.