refactor: rename rebuild subcommand to filter

Rename the `rebuild` CLI subcommand to `filter` to better reflect its primary purpose of row-level selection and k-mer filtering. Update all associated CLI arguments, logging, error messages, and module registrations accordingly. Introduce a dedicated `Rebuild` subcommand for index compaction, fully decoupling it from the filtering logic. Also refine related documentation to align with the new naming and semantics.

docmd/index.md

@@ -9,7 +9,7 @@
 | `superkmer` | Extract super-kmers from a sequence file and write to stdout |
 | `index`     | Build a complete genome index (scatter → dereplicate → count → layered MPHF) |
 | `merge`     | Merge multiple built indexes into one |
-| `rebuild` / `filter` | Filter and compact an existing index into a new single-layer index; supports the shared [kmer filtering](implementation/filtering.md) system (`filter` is an alias for `rebuild`) |
+| `filter` | Apply row-level selection (σ) to an index: retain only k-mers matching the ingroup/outgroup predicates. Output is a new single-layer index — compaction is a consequence, not the goal. Supports the shared [kmer filtering](implementation/filtering.md) system |
 | `query`     | Query an index with sequences and annotate matches |
 | `dump`      | Dump all indexed k-mers as CSV (kmer + per-genome counts or presence); supports the shared [kmer filtering](implementation/filtering.md) system; `--head N` limits output to the first N k-mers |
 | `annotate`  | Add or update genome metadata from a CSV file; or dump metadata as CSV |