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interesting read. The app-only model is indeed locking users into a den from where they is no escaping.
I think a lot of us thought the same thing when AOL, CompuServe and Prodigy brought us into their walled gardens. Things are cyclical. If you're on the upswing of the cycle, it can look like you're going to go up forever. If you step back and watch the ebb and flow of the cycle, though, you get a much clearer picture of where things are headed in the long run.
um, how will these apps work, without the internet?
We already had native applications. C64 applications. MS-DOS applications. Windows applications. Mac OS applications. Linux applications. Java applications.

Slow to deploy. Insecure. Hard to tinker with. Not standardized. Tied to one OS.

Then came the web and won.

Why should apps suddenly come back and take over?

My bet is on the web.

I want the web to win too.
I want freedom to win and if it only comes in the form of the web then I will settle for that.

Unfortunately capitalism motivates device manufacturers to try and build captive markets.

There currently are 2 issues the web has to overcome:

1) Via a manifest file, websites can be available offline. But currently, if people want a tool they "download an app". They don't add a website to their homescreen.

2) People can easily pay for an app. But not for a website.

Problem is phone manufacturers have a vested interest in making the web experience sub-optimal (and even limit developers' means of building a proper mobile browser, like Apple).
Apps are essentially a new form of the website as we know it now.
They are not. Apps are not like websites. Thats what I am trying to say here.
Yes they are. Your complaints in your article hardly signal the "end of the Internet".
No, for the reasons laid out in the article. Not least: websites (at least well designed ones) are platform agnostic.
I think the title is wrong, apps cannot kill the Internet but they can kill the Web.
The internet != hypertext/www.

Title of this should have been: "Is the app-only economy going to kill the web?".

To me, this is like asking is replacing the hand-cranks with electric starters going to kill the car engine.
Only one point to nitpick: let's stop spreading the "RSS is dead" meme. It's not. RSS/Atom are alive and well.

Google reader != RSS.

These standards are open and simple enough for everyone to implement on their site/blog, and they'll only die if we all start acting like they're dead because one company decided to phase out a product that was not even living up to its full potential. I use https://www.newsblur.com/ on a daily basis and it's a far superior piece of software.

If I ship an iOS or Android App, then my website will feature prominent graphical links to the app store and google play. I'll be passing on some of my pagerank to them. How much will the app store and google play pass back to me?

I don't see either the app store or google play as being in my long-term interest. It is very nearly impossible for app publishers to use alternative distribution channels such as direct mail.

I'm toying with the idea of rewriting my native Objective-C iOS App entirely in javascript, so it won't need to be in the app store. That would be a lot of work but I really do feel that, in the long run, Apple and Google are destroying the independent developers.