feat: introduce _iqtree_states.csv for compact symbol mapping

Generates a new CSV output that maps IQ-TREE's compact state symbols to canonical states alongside full-precision empirical frequencies. Updates documentation to clarify that state frequencies sum to 1.0 by design and documents conditional behavior under `--free-loss`. Includes unit tests verifying absent state exclusion, frequency summation, and CSV structure. Also restricts entropy annex resolution to non-monomorphic minorants to eliminate redundant per-genome checks.

doc/usage/phylo/index.html

@@ -2014,6 +2014,12 @@
 <td>FASTA</td>
 <td>alignment recoded for that model</td>
 </tr>
+<tr>
+<td><code>&lt;prefix&gt;_iqtree_states.csv</code></td>
+<td><code>--iqtree</code></td>
+<td>CSV table</td>
+<td>maps <code>_iqtree.model</code>/<code>_iqtree.fasta</code>'s compact state symbols back to <code>_sankoff_matrix.csv</code>'s alphabet</td>
+</tr>
 </tbody>
 </table>
 <p><strong><code>_sankoff_matrix.csv</code></strong> — header <code>state,0,A,C,M,G,R,S,V,T,W,Y,H,K,D,B,N</code>: the 16 symbols are IUPAC codes for the 16 subsets of the 4 possible central bases (bit 0=A, 1=C, 2=G, 3=T), <code>0</code> standing for the empty/absent state (not <code>-</code>, to avoid colliding with external tools' own gap syntax). One row per source state, one value per destination state, cost <span class="arithmatex">\(-\ln P(a,b)\)</span>, 4 decimals.</p>
@@ -2048,6 +2054,7 @@
 <p><strong><code>_iqtree.fasta</code></strong> (<code>--iqtree</code>) — alignment recoded to that same compact <code>0..k-1</code> alphabet (symbols <code>0-9A-F</code>). Under <code>--free-loss</code>, non-detection becomes <code>?</code> and columns left non-informative once missing calls are ignored are dropped first (required for <code>+ASC</code>). Run with:
 <div class="highlight"><pre><span></span><code>iqtree3 -s &lt;prefix&gt;_iqtree.fasta --seqtype MORPH -m &lt;prefix&gt;_iqtree.model+ASC --prefix &lt;prefix&gt;_iqtree -T AUTO
 </code></pre></div></p>
+<p><strong><code>_iqtree_states.csv</code></strong> (<code>--iqtree</code>) — one row per state actually kept in <code>_iqtree.model</code>/<code>_iqtree.fasta</code> (header <code>iqtree_symbol,canonical_symbol,frequency</code>): <code>iqtree_symbol</code> is the compact <code>0-9A-F</code> symbol as written in those two files, <code>canonical_symbol</code> is the matching <code>_sankoff_matrix.csv</code> state, <code>frequency</code> is that state's empirical frequency at full precision (<code>_iqtree.model</code>'s own frequency line is rounded to 6 decimals). Under <code>--free-loss</code>, absent (<code>0</code>/<code>?</code>) is never a kept state, so it never appears here. Use this file to identify which real state a given row/column of <code>_iqtree.model</code>'s matrix corresponds to — e.g. to check whether a state showing zero exchangeability with everything else is expected (a state combination that never co-occurs with anything else in this data) or worth investigating further.</p>