feat: add benchmark pipeline, expose APIs, and enforce strict paths

Introduces a Make-based orchestration for simulating, indexing, merging, filtering, and verifying k-mer counts and presence. Exposes internal builder and iterator APIs publicly, enforces mandatory leading slashes for predicate patterns, registers the `obitaxonomy` crate, and updates tooling configurations alongside documentation.

src/obikindex/src/merge.rs

@@ -11,7 +11,7 @@ use obilayeredmap::IndexMode;
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
 use crate::meta::{GenomeInfo, IndexMeta};
-use crate::state::IndexState;
+use crate::state::{IndexState, SENTINEL_INDEXED};
 
 pub use obikpartitionner::MergeMode;
 
@@ -263,6 +263,8 @@ impl KmerIndex {
             rep.push(t.stop());
         }
 
+        fs::File::create(output.join(SENTINEL_INDEXED)).map_err(OKIError::Io)?;
+
         KmerIndex::open(output)
     }
 }