They can’t be used yet from WebExtensions, only from bootstrap and Addon SDK addons right now. Hopefully native.js comes around soon though.
This brings some hope. Currently we use both ctypes and chrome components to call cryptographic API (crypt32.dll) and also use printing services to print with custom preferences on custom printer from our web application but it doesn’t seem any of it is possible with WebExtensions.
Currently extensions are both powerful and easy to install while they need to be accpeted by user anyway. I also hope that automatic siging will always be possible for unpublished addon even with native.js or anything like that.
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I consider native messaging in best case as a emergency solution and that in all use cases. Why? You need to setup the app manifest and registry settings on the host computer. Comment end.
I’m playing at the moment with webextensions experiments for child process based on sdk child_process. It works. But of course there is no use case if you need a nightly here.
Yes, it’s solution that would work but that would require installing additional software on every client’s PC just as TheRave said. Which isn’t as simple as showing a link “press here to install extension” in our application after logging in.