I've found a problem with the current MobiUnpack. A Mobipocket link is usually given in the source as something like
<a filepos=0000005027 >
I've come across some that also have an id attribute like this
<a id="When" filepos=0004135413 >
MobiUnpack is correctly converting the first into an href <a href="#filepos5027" > and inserting an anchor links <a id="filepos5027" />
Unfortunately, for the second form, although an anchor link is successfully inserted, the original mobipocket link isn't converted into an href.
I'm looking into this now myself, but if anyone has any ideas for a fix, I'd be glad to hear them!
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