feat: add merge command to consolidate k-mer indexes

Introduces a new `merge` CLI subcommand and underlying implementation to consolidate multiple pre-indexed k-mer indexes into a single output. Adds `append_column` methods to persistent bit and int matrices to enable incremental genome column expansion without rebuilding the MPHF. Includes new error variants for index readiness and configuration mismatches, adds a `--force` flag to the index command, and updates documentation and navigation structure accordingly.

src/obicompactvec/src/bitmatrix.rs

@@ -101,6 +101,26 @@ impl PersistentBitMatrix {
     }
 }
 
+// ── Column append ─────────────────────────────────────────────────────────────
+
+impl PersistentBitMatrix {
+    /// Append a new column to an existing matrix on disk.
+    ///
+    /// Reads `meta.json` to obtain `n` and the current column count, writes
+    /// `col_{n_cols:06}.pbiv` filled by `value_of(slot)`, then increments
+    /// `n_cols` in `meta.json`.
+    pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
+        let mut meta = MatrixMeta::load(dir)?;
+        let mut b = PersistentBitVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
+        for slot in 0..meta.n {
+            b.set(slot, value_of(slot));
+        }
+        b.close()?;
+        meta.n_cols += 1;
+        meta.save(dir)
+    }
+}
+
 fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
     (0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
 }

src/obicompactvec/src/intmatrix.rs

@@ -203,6 +203,26 @@ where
     m
 }
 
+// ── Column append ─────────────────────────────────────────────────────────────
+
+impl PersistentCompactIntMatrix {
+    /// Append a new column to an existing matrix on disk.
+    ///
+    /// Reads `meta.json` to obtain `n` and the current column count, writes
+    /// `col_{n_cols:06}.pciv` filled by `value_of(slot)`, then increments
+    /// `n_cols` in `meta.json`.
+    pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> u32) -> io::Result<()> {
+        let mut meta = MatrixMeta::load(dir)?;
+        let mut b = PersistentCompactIntVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
+        for slot in 0..meta.n {
+            b.set(slot, value_of(slot));
+        }
+        b.close()?;
+        meta.n_cols += 1;
+        meta.save(dir)
+    }
+}
+
 // ── Trait impls ───────────────────────────────────────────────────────────────
 
 use crate::traits::{ColumnWeights, CountPartials};