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 Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.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 = "1.3.1"
+version = "1.2.3"
 dependencies = [
  "clap",
  "csv",

src/obikdump/Cargo.toml

@@ -11,5 +11,5 @@ obikseq       = { path = "../obikseq" }
 obidebruinj   = { path = "../obidebruinj" }
 obifastwrite  = { path = "../obifastwrite" }
 obicompactvec = { path = "../obicompactvec" }
-obisys        = { path = "../obisys", default-features = false }
+obisys        = { path = "../obisys" }
 rayon         = "1"

src/obikfilter/Cargo.toml

@@ -14,5 +14,5 @@ obikidxcache  = { path = "../obikidxcache" }
 obikindexer   = { path = "../obikindexer" }
 obidebruinj   = { path = "../obidebruinj" }
 obikalgorithm = { path = "../obikalgorithm" }
-obisys        = { path = "../obisys", default-features = false }
+obisys        = { path = "../obisys" }
 tracing       = "0.1.44"

src/obikindex/Cargo.toml

@@ -7,7 +7,7 @@ edition = "2024"
 obikseq          = { path = "../obikseq" }
 obitaxonomy      = { path = "../obitaxonomy" }
 obiskio          = { path = "../obiskio" }
-obisys           = { path = "../obisys", default-features = false }
+obisys           = { path = "../obisys" }
 obicompactvec    = { path = "../obicompactvec" }
 obidebruinj      = { path = "../obidebruinj" }
 obipipeline      = { path = "../obipipeline" }

src/obikindexer/Cargo.toml

@@ -9,7 +9,7 @@ obikalgorithm    = { path = "../obikalgorithm" }
 obikseq          = { path = "../obikseq" }
 obidebruinj      = { path = "../obidebruinj" }
 obiskio          = { path = "../obiskio" }
-obisys           = { path = "../obisys", default-features = false }
+obisys           = { path = "../obisys" }
 obicompactvec    = { path = "../obicompactvec" }
 obipipeline      = { path = "../obipipeline" }
 obiread          = { path = "../obiread" }

src/obikmer/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.3.1"
+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" }

src/obikmerge/Cargo.toml

@@ -11,7 +11,7 @@ obicompactvec = { path = "../obicompactvec" }
 obiskio       = { path = "../obiskio" }
 obikseq       = { path = "../obikseq" }
 obipipeline   = { path = "../obipipeline" }
-obisys        = { path = "../obisys", default-features = false }
+obisys        = { path = "../obisys" }
 rayon         = "1"
 tracing       = "0.1.44"
 

src/obikphylo/Cargo.toml

@@ -7,7 +7,7 @@ edition = "2024"
 obikindex        = { path = "../obikindex", default-features = false }
 obikseq          = { path = "../obikseq" }
 obiskio          = { path = "../obiskio" }
-obisys           = { path = "../obisys", default-features = false }
+obisys           = { path = "../obisys" }
 obicompactvec    = { path = "../obicompactvec" }
 obikidxcache     = { path = "../obikidxcache" }
 obiskbuilder     = { path = "../obiskbuilder" }

src/obikrebuild/Cargo.toml

@@ -10,5 +10,5 @@ obikfilter    = { path = "../obikfilter" }
 obikidxcache  = { path = "../obikidxcache" }
 obikseq       = { path = "../obikseq" }
 obidebruinj   = { path = "../obidebruinj" }
-obisys        = { path = "../obisys", default-features = false }
+obisys        = { path = "../obisys" }
 tracing       = "0.1.44"

src/obikselect/Cargo.toml

@@ -8,5 +8,5 @@ obikindex     = { path = "../obikindex" }
 obikfilter    = { path = "../obikfilter" }
 obikalgorithm = { path = "../obikalgorithm" }
 obicompactvec = { path = "../obicompactvec" }
-obisys        = { path = "../obisys", default-features = false }
+obisys        = { path = "../obisys" }
 tracing       = "0.1.44"