ios and web is part of FM. No reason to move from your FM app. You can have one file or separate files that link to the same data source. Any of the starter solution startup script will show you how to detect which device / platform your app is running.
On ios device you can use FMGo with a webclip to launch your database in FMGo or you can use the new iosAppSDK. The iosAppSDK requires xcode which is only available on a MAC.
Some script steps work differently on ios and webdirect and then there are some script steps that works only on that platform, then some script triggers do not work in web direct, so you will need to test your app on each platform.
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For prototyping a web application, I have not really used FMP to any real extent since it doesn't have many of the rich controls of modern web applications.
You therefore might be just as well off using a tool like "ForeUI" or another screen prototyping tool. It will even create a "working" navigation between screens. There are other similar tools.
I have not used FM for "proto-typing", but if what I'm doing (per client) needs to be "native iOS" or full-web, then it because of any "limitations" in FM (PRO, GO, & WD) with or without FMServer. It's a matter of using the better tool for the task. But often it's just a bigger phase to a project and FM may stay in the mix as well.
I have a similar question. Do you have any updates on what you've learned?