chore: remove completed migration anchors

[zimakki]

Summary

• remove the 19 root compatibility symlinks and both one-time JSON snapshots after both managed Macs verified direct static links and regular app-owned JSON files
• retire the static relinker and the cutover-only Lazygit and JSON-overlay symlink normalization paths
• update current docs and tests for the steady-state app-oriented layout while retaining canonical-checkout guards, conflict refusal, declarative ownership, overlay preservation, failure propagation, and convergence checks

Both zis-AccessOwl-MacBook-Pro and zis-MacBook-Pro completed the migration and passed repeated verification before this contraction. The remaining live Homebrew drift is unrelated and this PR does not change BrewFile.

Validation

• scripts/ci_checks.sh
• stale-reference audit for removed anchors, snapshots, migration helper, and completed cutover guidance
• confirmed no tracked top-level symlinks or legacy snapshots remain