refactor: extract obikindex crate and remove deprecated CLI commands

Extracted core indexing logic, state tracking, and metadata management into a new `obikindex` crate. Refactored the `index` and `unitig` commands to leverage the `KmerIndex` abstraction and state-driven pipeline transitions. Removed obsolete CLI subcommands (`count`, `fasta`, `longtig`, `partition`) and their associated pipeline steps. Updated FASTA writing utilities for single-line output and deterministic identifiers, and refreshed workspace dependencies.

src/obikindex/Cargo.toml

@@ -0,0 +1,21 @@
+[package]
+name = "obikindex"
+version = "0.1.0"
+edition = "2024"
+
+[dependencies]
+obikpartitionner = { path = "../obikpartitionner" }
+obikseq          = { path = "../obikseq" }
+obisys           = { path = "../obisys" }
+obiskio          = { path = "../obiskio" }
+obidebruinj      = { path = "../obidebruinj" }
+obilayeredmap    = { path = "../obilayeredmap" }
+obicompactvec    = { path = "../obicompactvec" }
+cacheline-ef     = "1.1"
+epserde          = "0.8"
+ptr_hash         = "1.1"
+rayon            = "1"
+serde            = { version = "1", features = ["derive"] }
+serde_json       = "1"
+indicatif        = "0.17"
+tracing          = "0.1.44"