chore(a2ml-migration): remove legacy .scm checkpoint files

6a2/ counterparts (ECOSYSTEM.a2ml, META.a2ml, STATE.a2ml) already exist
in .machine_readable/6a2/ — these .scm files are superseded legacy.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: hyperpolymath