refactor: Shift KmerIndex ownership to Arc for thread-safe sharing

Replaces lifetime-bound references with runtime reference counting across multiple crates. This enables safe concurrent access across parallel workers without explicit cloning or manual lifetime management. Introduces the `query` and `utils` CLI commands in obikmer2, along with supporting modules for batch processing, sparse indexing, sliding-window findere logic, and output formatting. Updates dependency manifests and aligns test suites with the new ownership model.

src/Cargo.lock

@@ -1673,12 +1673,16 @@ dependencies = [
  "obikalgorithm",
  "obikdump",
  "obikfilter",
+ "obikidxcache",
  "obikindex",
  "obikindexer",
  "obikmerge",
+ "obikquery",
  "obikrebuild",
+ "obikrope",
  "obikselect",
  "obikseq",
+ "obikstats",
  "obipipeline",
  "obiread",
  "obiskbuilder",
@@ -1732,7 +1736,15 @@ dependencies = [
 name = "obikquery"
 version = "0.1.0"
 dependencies = [
+ "obikidxcache",
  "obikindex",
+ "obikrope",
+ "obikseq",
+ "obiread",
+ "obiskbuilder",
+ "serde_json",
+ "tempfile",
+ "tracing",
 ]
 
 [[package]]