Don't assume unique repo names in ecosystem checks (#4628)
This fixes a bug where previously repositories with the same name would have been overwritten.
I tested with `scripts/check_ecosystem.py -v --checkouts target/checkouts_main .venv/bin/ruff target/release/ruff` and ruff 0.0.267 that changes are shown. I confirmed with `scripts/ecosystem_all_check.sh check --select RUF008` (next PR) that the checkouts are now complete.
