Tidy the repository: remove docs/research and bench, fix references

SIMURGARRAY_MASTER_PLAN.md

@@ -221,7 +221,6 @@ simurg/
 ├── tests/
 │   ├── unit/ property/ integration/ regression/ oracle/ perf/
 │   └── fixtures/             # ONLY redistributable data (Bioconductor Artistic-2.0 files, synthetic)
-├── bench/
 ├── docs/                     # user guide, algorithm notes, validation reports
 ├── refs/                     # (git-ignored) cloned third-party repos
 └── data/                     # (git-ignored) downloaded datasets