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It will always be the last App you opened, so if you open another App such as the Spreadsheet or whatever, then that will appear in the program list in its place. It is NOT a bug. It allows you to create or edit a program that appears in the App screen and is actually a pretty neat feature.
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Function App is part of the built in OS just as Finance, Geometry and etc.
Select another app, say geometry. Then go to the Program library and you will see the new app listed at the top of the screen above your other programs.
You cannot remove the new app listed at the top of the program screen. It will always reflect the last selected app from the app screen.
Unless I am missing something in your question.
Geoff
Michael and I were typing at the same time, he beat me to the post button :-0
Edited: 6 Nov 2013, 1:16 a.m.
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As Michael and Geoff have already stated, the program is tied to the application just started. It can be modified to change the behavior of the application (redefine views and such). This makes most sense if you SAVE the application under a different name (which will create a shallow copy of the app). This is the way custom applications can be created on the device.
What's missing is an SDK to create an application from scratch. On the predecessors of the Prime and the 39gs II, namely the 38G and 39G (and the siblings 39gs, 40G and 40gs), you could do it in SysRPL. On the Prime this will most probably be C++. The ancient ADK for the 38/39 series can be compared to the Connectivity Kit of the Prime: Apps created with this tool on the PC use only user level programming.
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Well I be darned, you guys are right. That's why I hang here so much. Thank you for setting my mind at ease!