Release 2.0.0: v2 modules (ArrayTrain, CN/LOH, PGx, methylation QC)

User guide: ArrayTrain section, v2 commands in the table, v2 accuracy rows,
updated limitations. README status for v2.0.0. Version 2.0.0 (Python package);
the Rust kernels are unchanged and stay simurg_core 1.1.0. uv.lock committed
(uv lock --check clean).

Full suite on the Pi, file by file under the memory guard: 29 files exit 0
(unit: 282 passed), ruff and mypy clean.

src/simurg/__init__.py

@@ -4,5 +4,5 @@ Specification: SIMURGARRAY_MASTER_PLAN.md (algorithms, roadmap) and
 SIMURGARRAY_FUNCTIONAL_SPEC.md (externally visible behaviour, item IDs such as CLI-021).
 """
 
-__version__ = "1.1.0"
+__version__ = "2.0.0"
 PRODUCT_NAME = "SimurgArray"