There are additional APIs available to all applications. They don't need to come from the marketplace to use such APIs. An application can use the "Open Web Apps API" to install itself onto the phone (with the user permission) bypassing the marketplace. So you can distribute your own apps on third party marketplaces or on your own web page.
There are two types of applications: Hosted and Packaged. Hosted apps are normal web pages that you host somewhere and access from the device. If you use appcache and responsive design, they will provide an experience like what native apps provide in other platforms. The packaged apps instead of being hosted are packaged and offered on the marketplace. Its basically a zipfile with your HTML/CSS/JS, when it is installed this zipfile is copied to the device and sandboxed.
There are three security levels. Plain, Privileged and Certified. These security levels govern what APIs your app can access. Hosted apps are always plain apps. Packaged apps can be plain apps too but they can also be privileged apps that can access an extra set of APIs or certified apps that can access every API on the device. Only Mozilla and its hardware partners can build and deploy certified apps due to security reasons (you don't want an app with the ability to send SMS or make calls without user interaction).
So in summary, you can have plain web links in the launcher and you can have links to packaged apps that are actually on the device. Both things are possible and indistinguishable from a user point of view. Both solutions work offline if you use appcache with the hosted app.
Given that the post we're all discussing is from someone who is ostensibly pretty savvy about these things, I think it might behoove the folks working on Firefox OS to rethink aspects of the platform user experience.
There are two types of applications: Hosted and Packaged. Hosted apps are normal web pages that you host somewhere and access from the device. If you use appcache and responsive design, they will provide an experience like what native apps provide in other platforms. The packaged apps instead of being hosted are packaged and offered on the marketplace. Its basically a zipfile with your HTML/CSS/JS, when it is installed this zipfile is copied to the device and sandboxed.
There are three security levels. Plain, Privileged and Certified. These security levels govern what APIs your app can access. Hosted apps are always plain apps. Packaged apps can be plain apps too but they can also be privileged apps that can access an extra set of APIs or certified apps that can access every API on the device. Only Mozilla and its hardware partners can build and deploy certified apps due to security reasons (you don't want an app with the ability to send SMS or make calls without user interaction).
So in summary, you can have plain web links in the launcher and you can have links to packaged apps that are actually on the device. Both things are possible and indistinguishable from a user point of view. Both solutions work offline if you use appcache with the hosted app.
If you want to know more, I've written a Free and Open eBook about it called "Firefox OS Development Quick Guide" available at http://leanpub.com/quickguidefirefoxosdevelopment/ you can also hop by Mozilla Developer Network portal for Firefox OS at https://developer.mozilla.org/en-US/Firefox_OS
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