docs: expand kmer indexing, filtering, and merging documentation

Expands MkDocs navigation and documentation for evidence elimination, the merge command, and kmer filtering. Refactors kmer representation to a generic `KmerOf<L>` type with a bitwise reverse complement algorithm. Unifies MPHF construction, introduces approximate fingerprint-based indexing, and updates the pipeline, chunkreader, and storage layouts. Adds code coverage reports and clarifies architectural invariants for improved maintainability.

doc/theory/encoding/index.html

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+    Evidence elimination (discussion)
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+      <a href="../../implementation/merge/" class="md-nav__link">
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+    Merge command
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+    Kmer filtering (rebuild/dump/unitig)
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@@ -1010,17 +1094,20 @@
 <p>The Watson-Crick complement of any base is its bitwise NOT on 2 bits: <code>complement(base) = ~base &amp; 0b11</code>.</p>
 <h2 id="kmer-encoding">Kmer encoding</h2>
 <p>A kmer fits in a single <code>u64</code>. Nucleotide 0 occupies bits 63–62, nucleotide i occupies bits 63−2i and 62−2i, and the low 64−2k bits are zero. Extraction of nucleotide i (0 ≤ i &lt; k): <code>(kmer &gt;&gt; (62 - 2*i)) &amp; 0b11</code>.</p>
-<p>Reverse complement is computed via a <strong>16-bit lookup table</strong> (65 536 entries × 2 bytes = 128 KB, fits in L2 cache) storing the reverse-complement of every 8-base chunk.</p>
+<p>Reverse complement is computed by <strong>bit manipulation in four steps</strong>, with no lookup table:</p>
 <div class="admonition abstract">
 <p class="admonition-title">Algorithm — Kmer reverse complement</p>
 <div class="highlight"><pre><span></span><code>procedure KmerRevcomp(kmer, k):
-    raw ←   TABLE16[kmer &amp; 0xFFFF]         &lt;&lt; 48
-          | TABLE16[(kmer &gt;&gt; 16) &amp; 0xFFFF] &lt;&lt; 32
-          | TABLE16[(kmer &gt;&gt; 32) &amp; 0xFFFF] &lt;&lt; 16
-          | TABLE16[(kmer &gt;&gt; 48) &amp; 0xFFFF]
-    return raw &lt;&lt; (64 - 2*k)
+    x ← ~kmer                                           -- complement all bases
+    x ← swap_bytes(x)                                   -- reverse byte order
+    x ← ((x &gt;&gt; 4) &amp; 0x0F0F0F0F0F0F0F0F)
+       | ((x &amp; 0x0F0F0F0F0F0F0F0F) &lt;&lt; 4)               -- swap nibbles within each byte
+    x ← ((x &gt;&gt; 2) &amp; 0x3333333333333333)
+       | ((x &amp; 0x3333333333333333) &lt;&lt; 2)                -- swap 2-bit pairs within each nibble
+    return x &lt;&lt; (64 - 2*k)                              -- re-align to MSB
 </code></pre></div>
 </div>
+<p>The three reorder passes together reverse the order of all 2-bit base codes across the 64-bit word. The bitwise NOT in the first step complements each base (A↔T, C↔G). The final left shift clears the low 64−2k padding bits.</p>
 <p>The <strong>canonical form</strong> is the lexicographic minimum of the kmer and its reverse complement:</p>
 <div class="highlight"><pre><span></span><code>canonical(kmer) = min(kmer, revcomp(kmer))
 </code></pre></div>