rename hit_matrix/raw_hit_matrix

For clarity: the result from make_hit_matrix should be in
$raw_hit_matrix, then the best results should be put into $hit_matrix.
findsequences can just return the hash directly.

It is pointless for findsequences to unhash its results into an array:
should just return the hash itself.
$hit_matrix should be cumulative, but can keep separate array of @contig_names for this iteration's results.