Preserve Species-GA population under clone backfill

[isty2e]

Summary

Fixes #27.

Species-GA survival now tracks protected members by their pool index instead of dataclass value equality. Clone-heavy pools can therefore backfill with distinct pool entries even when candidates, values, and scores are equal. The same survival pass also prioritizes species seeds before same-species crowd members when protected entries exceed population_size.

Root cause

The backfill path used member not in protected_population, which calls dataclass equality. In clone-heavy generations, every value-equal clone was excluded from backfill, so the population could shrink below population_size and later fail tournament selection. The truncation path also sliced protected entries in flatten order, which could drop a later species seed behind an earlier species crowd member.

Validation

• uv run --python 3.11 --extra test pytest tests -q
• uv run --python 3.11 --extra test ruff check pyproject.toml src tests
• uv run --python 3.11 --extra test basedpyright src tests
• uv run --python 3.11 --extra test mypy src/variopt still reports the existing scipy/joblib missing-stub errors only.