The memory of the DR is split in two parts, the internal flash of the DR itself and the SD-card(s) that you insert yourself. Until now, every firmware update replaces the complete content of the internal flash and thus erases everything installed on it.
The programs written/ported by 3rd party developers can be installed on SD only, on flash only or a combination (like FBReader). So when you upgrade the firmware the parts that are on internal flash need to be re-instelled.
It is possible that iRex will provide a method in the future so that user-installed programs on flash will 'survive' but until now this is not possible.
FBReader has a special thing, it also updates a 'core component' of the DR firmware, the Content Browser (ctb). iRex has published (most of) the code of the firmware, so anyone can make extensions to it. The change made to the ctb, adds the functionality that files associated with FBReader will automatically start the FBreader when you tap on them in the Content Browser (the Content Browser is what you see after you started the DR).
To come to your questions:
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My brand new DR1000S is at 1.6, so should I wait for a 1.6 build?
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I think you should wait for changed ctb (if needed) for R1.6, since some small changes are made in the code that you will not have when you are using the changed R1.5 version.
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Is this a repeating cycle?
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See above, currently it is (for the ctb part), although there is a change in R1.6 which seems to make the link between extension and application configurable without compiling code.
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Also, is this download the complete package I need, or do I go get the FBReader program itself from elsewhere?
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You you need to install both the FBReader and the Content Browser (ctb) patch. Without Content Browser patch, you need to start FBReader and open the files you want to read manually, with the patch you can tap on the file and it will open in FBReader. See also
here for info on other programs.
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Pardon my ignorance, I'm a brand new DR1000S owner looking to get .chm going.
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Lets hope I made you a little wiser
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