docs: add obikmer user guide and MkDocs build configuration

Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.
2026-08-13 17:19:01 +02:00
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+# dump
+
+Dump all kmers of an index as CSV, one row per kmer, with per-genome counts or presence.
+
+```bash
+obikmer dump INDEX [OPTIONS]
+```
+
+## Arguments
+
+| Argument | Description |
+|---|---|
+| `INDEX` | Index directory to dump |
+
+## Options
+
+| Option | Default | Description |
+|---|---|---|
+| `--force-presence` | off | Output presence/absence (0/1) even if the index stores counts |
+| `--debug` | off | Prefix each row with the partition and layer columns |
+| `--head N` | none | Limit output to the first N kmers |
+
+`dump` also accepts the shared [predicate options](filter.md#predicate-options) (`--ingroup`, `--outgroup`, `--min-count`, etc.) to restrict which kmers are dumped.
+
+Output is CSV on stdout.