refactor(benchmark): consolidate generated artifacts under run/ directory

Restructure the benchmark pipeline to direct all simulated data, indices, statistics, and query outputs into a unified `run/` directory. Update Makefile targets, shell scripts, and Python utilities to resolve paths relative to this new base. Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.

src/Cargo.lock

@@ -1480,7 +1480,7 @@ dependencies = [
 
 [[package]]
 name = "obikmer"
-version = "1.3.0"
+version = "1.2.3"
 dependencies = [
  "clap",
  "csv",

src/obikmer/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.3.0"
+version = "1.2.3"
 edition = "2024"
 
 [[bin]]
@@ -11,7 +11,7 @@ path = "src/main.rs"
 obikseq       = { path = "../obikseq" }
 obiread       = { path = "../obiread" }
 obipipeline   = { path = "../obipipeline" }
-obisys        = { path = "../obisys", default-features = false }
+obisys        = { path = "../obisys" }
 obikindex     = { path = "../obikindex", default-features = false }
 obikindexer   = { path = "../obikindexer" }
 obikalgorithm = { path = "../obikalgorithm" }