Implement pack CLI command for matrix packing and layer compaction

Adds the `pack` subcommand to `obikmer2` for persisting presence and count matrices in sparse or dense formats. Introduces the `compact_layer` module in `obikrebuild` to merge multiple partition layers into a single layer in-place via atomic operations. Updates dependencies across `obikdump`, `obikmer2`, and `obikrebuild` to resolve new local crate references. Shifts the architecture from multi-layer accumulation to in-place compaction, removing legacy rebuild modules.

src/Cargo.lock

@@ -1523,12 +1523,14 @@ version = "0.1.0"
 name = "obikdump"
 version = "0.1.0"
 dependencies = [
+ "obicompactvec",
  "obidebruinj",
  "obifastwrite",
  "obikfilter",
  "obikidxcache",
  "obikindex",
  "obikseq",
+ "obisys",
  "rayon",
 ]
 
@@ -1674,6 +1676,7 @@ dependencies = [
  "obikindex",
  "obikindexer",
  "obikmerge",
+ "obikrebuild",
  "obikselect",
  "obikseq",
  "obipipeline",
@@ -1736,14 +1739,12 @@ dependencies = [
 name = "obikrebuild"
 version = "0.1.0"
 dependencies = [
- "obicompactvec",
  "obidebruinj",
  "obikfilter",
+ "obikidxcache",
  "obikindex",
  "obikindexer",
- "obikmerge",
  "obikseq",
- "obiskio",
  "obisys",
  "tracing",
 ]