Overhaul rfreplace.pl script for new independent SEED paradigm

[nawrockie]

This was originally motivated by a suggestion from Franz Lang that users should not need to enforce the Rfam convention for sequence names in SEED alignments - a script should be able to do that. Anton suggested rfreplace could do that. After looking at current rfreplace code it is clear it needs to be scrapped and rewritten anyway for the new independent SEED paradigm (SEED seqs now only need to be in GenBank/RNAcentral as opposed to in Rfamseq (old paradigm)). Whereas current rfreplace looked only at hits in Rfamseq as candidates for replacing existing SEED seqs, we can now look at all seqs in GenBank/RNAcentral. Getting back to Franz's suggestion, if a sequence is found that is 100% identical in GenBank/RNAcentral that sequence's name can be used to rename the sequence in the input SEED.