It's an interesting discussion here, for me. I agree most of the ideas contributed here:
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I do like your suggestion of a fixed filesystem at /opt, but it isn't that different form Adam B's suggestion, simply /opt instead of /home/root/Apps, personally I prefer /opt. However, I still prefer a distributed approach with symlinks rather than placing the opt directory on the card.
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I agree.
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The final problem is to do with the 'unbrickability' of it; for some programs the reason the root filesystem must be modified, is to support the contentlister, or to add new fonts/etc (as in AbiWord); these would both not be 'fixed' by the use of an /opt directory, not saying the alternative works - but just pointing out a limitation.
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When a unbrickable solution given, I'm sure this can be solved. If contentlister becames more flexible to allow us add our stuff, can help but this is a iRex alternative and no way until they do the next move and show us their solution to unbrickability.
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The setup script I would propose would work like this:
[0) Extract the archive in-place]
1) Create /opt/programs if it does not exist - *on* the root filesystem
2) Symlink /opt/programs/fbreader to the location of this script.
3) Create a _libs directory on whatever medium is used (be in CF/MMC/root) if it does not exist.
4) Optionally, move any required libraries to the _libs directory
5) Delete any libraries from the package that are contained within _libs (if you do step #4, this implies deleting all libraries).
6) Run the program.
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This is good to me, but the fourth point I'm not sure how to deal with it. It has been discussed to use a common /opt/lib directory, and is the better for me, but since this will fast decrease free internal memory, a _libs on cards looks good for me.

But don't understand your solution to avoid duplicated libs. Maybe I'm lost on translation?
Anyway, I will be aware to what you guys say on this thread and I will help in all I can!