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Frankly it seems easier to make indexing more resource sensitive than find a way to merge indexes of files from multiple file systems onto the Kindle.
A few simple changes:
If device is in use and there are pending indexing jobs, only index the current file. If the user does a search, put up a message and let them choose.
Only index when idle. Stop when battery goes to 50%. That way if it's idle and plugged in, it can index it's little heart out.
It doesn't make much sense to put a huge amount of development work to solve a problem most users don't experience and the users that do only experience rarely. Seriously. How often do you move 100+ books to your Kindle?
It reminds me of an old engineering story which may be apocryphal. The American astronauts complained that they couldn't use their pens while in space. NASA spent months of research and over a million dollars to design a pen that could work at zero gravity. The Russians gave their cosmonauts pencils.
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