Fix read count #4
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…f relying on block_index calculation (which differs between versions of PNut)
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The way repeat loop indices are left at the end of loop varies between compilers, even between PNut versions. Here's a change that explicitly counts the bytes as they are read. I think this makes the logic a bit clearer, as a bonus (but YMMV).
I also had to restore a change to RT_utilities to explicitly initialize the directory ID before looping through directory calls; flexspin will usually insert implicit initialization to 0, but for variables that are passed by address to subroutines.