Add unified matrix builder abstraction and k-mer filtering CLI

Introduces a unified MatrixBuilder abstraction for persistent bit and integer matrices, replacing custom dispatch enums and boolean flags across consumers. Refactors index, merge, and select layers to adopt explicit merge modes and centralized lifecycle management. Adds a complete k-mer filtering implementation with partition-level processing, progress tracking, and a new CLI subcommand supporting configurable predicates and thresholds.

src/Cargo.lock

@@ -1542,12 +1542,17 @@ name = "obikfilter"
 version = "0.1.0"
 dependencies = [
  "obicompactvec",
+ "obidebruinj",
+ "obikalgorithm",
  "obikentropy",
  "obikidxcache",
  "obikindex",
+ "obikindexer",
  "obikseq",
  "obiskio",
+ "obisys",
  "obitaxonomy",
+ "tracing",
 ]
 
 [[package]]
@@ -1662,6 +1667,7 @@ dependencies = [
  "csv",
  "obifastwrite",
  "obikalgorithm",
+ "obikfilter",
  "obikindex",
  "obikindexer",
  "obikmerge",