Extract k-mer counting logic into a dedicated counter module

Decouple k-mer counting from the partitioner by introducing a new `Counter` struct. The module exposes a fluent builder API with optional partial file retention, executes partition processing in parallel via Rayon with memory-aware chunk sizing, and integrates thread-safe progress callbacks. Update all callers to use the new counter, simplify test pipelines by removing serialization overhead, and clarify algorithm separation in module documentation.

.gitignore

@@ -4,6 +4,7 @@
 .kilo/
 .serena/
 .zed/
+.ast-cache/
 memory/
 sandbox/
 src/target