This is what they should have done. Instead, they chose to distribute a binary of their proprietary (patent pending [0]), closed source [1] product.
Not only am I not surprised that Apple shut them down the very next day, but I'm also having trouble feeling any sympathy for their cause.
[0] https://justgetflux.com/ - bottom of page
Commercial software is unlikely to be a trojan. You have much higher value as a paying customer than as a victim.
Open source software is similarly unlikely to be a trojan, especially if compiled from source.
Closed-source freeware is the perfect attack vector. Opaque and widely disseminated. Who knows what's going on inside? Freeware is responsible for a gigantic amount of malware.
There are no zero-risk activities, only risk signals. Some people choose to trust a corporation with lawyers and endless pages of EULA, some people choose to trust one authenticated developer with a proven track record of service to the community. At the moment, we are still free to make our own informed choices.
Open source is fine. If f.lux published the source code, then we could compile it ourselves, and Apple would be happy (they recently made the iOS Dev Program free of charge to allow sideloading in this manner.)
If iOS's app sandbox is inadequate, then those are all threats too, but Apple doesn't seem to mind them. If the sandbox is adequate, then apps like f.lux are safe even if intended to be malicious.
Apple's position is only really understandable if they don't understand their own technology. Which considering who is probably making these decisions could very well be true.
Apple does the same with their own products.
sending binaries you have to sign yourself.. I doubt that somewhat, they'll be signed by Apple.
For FOSS they use: http://www.opensource.apple.com
Not seeing anything about patents at that link.
And also, what in the world does "Proprietary, with free download. (with patent claim)" mean??
I remember this coming up on tech news sites a few years ago when I discovered f.lux... this article also makes mention of the patent-pending nature of the software: http://readwrite.com/2013/09/23/flux-a-hack-for-your-devices...