add name-tree command and fix --free-loss cost matrix

Introduce the obikmer name-tree subcommand to map numeric leaf labels in phylogenetic tree exports back to taxon names using a reference FASTA file. Correct the --free-loss flag behavior by removing cardinality transition costs from pairwise cost calculations, ensuring sibling gains and losses are priced identically to whole-family events. Update documentation, configuration parameters, and add reference phylogenetic data files.

iqtree.splits.nex

@@ -0,0 +1,62 @@
+#nexus
+
+BEGIN Taxa;
+DIMENSIONS ntax=13;
+TAXLABELS
+[1] 'Escherichia_coli--CFT073'
+[2] 'Escherichia_coli--EDL933'
+[3] 'Escherichia_coli--K-12_MG1655'
+[4] 'Escherichia_coli--K-12_W3110'
+[5] 'Klebsiella_pneumoniae--ATCC_13883'
+[6] 'Klebsiella_pneumoniae--HS11286'
+[7] 'Klebsiella_pneumoniae--MGH_78578'
+[8] 'Proteus_mirabilis--HI4320'
+[9] 'Salmonella_enterica--AKU_12601'
+[10] 'Salmonella_enterica--CT18'
+[11] 'Salmonella_enterica--LT2'
+[12] 'Salmonella_enterica--P125109'
+[13] 'Yersinia_ruckeri--YRB'
+;
+END; [Taxa]
+
+BEGIN Splits;
+DIMENSIONS ntax=13 nsplits=34;
+FORMAT labels=no weights=yes confidences=no intervals=no;
+MATRIX
+	100	 2,
+	100	 3,
+	100	 4,
+	100	 3 4,
+	69	 2 3 4,
+	100	 5,
+	100	 7,
+	16	 5 7,
+	100	 6,
+	100	 13,
+	16	 6 13,
+	23	 5 6 7 13,
+	100	 8,
+	100	 10,
+	23	 8 10,
+	100	 9,
+	100	 11,
+	100	 12,
+	100	 11 12,
+	100	 9 11 12,
+	23	 8 9 10 11 12,
+	100	 1 2 3 4,
+	100	 1,
+	84	 7 13,
+	83	 5 7 13,
+	77	 6 8,
+	76	 5 6 7 8 13,
+	76	 9 10 11 12,
+	31	 1 2,
+	1	 5 6 7 8,
+	1	 10 13,
+	1	 9 10 11 12 13,
+	1	 5 6 13,
+	1	 5 6 8,
+;
+END; [Splits]
+