Clear setup state before check

[codeforester]

Summary

• Clear inherited setup state at the start of basectl check before parsing check-specific flags.
• Add regression coverage for ambient DRY_RUN=true and BASE_SETUP_RECREATE_VENV=true leaking into check.
• Remove the completed TODO item.

Validation

• bats cli/bash/commands/basectl/tests/setup.bats
• bats cli/bash/commands/basectl/tests/basectl.bats
• bash -n cli/bash/commands/basectl/subcommands/check.sh
• git diff --check