learn: replace CLAUDE_SKIP_PERMISSIONS with trust-gate
Remove all references to CLAUDE_SKIP_PERMISSIONS env var and
process.argv --dangerously-skip-permissions check. Replace with
shouldBypassVet() from trust-gate module.
Error messages now include dangerous-accept hint when agent detected.
--user install still always requires explicit vetting regardless of
dangerous-accept.
Breaking change: CLAUDE_SKIP_PERMISSIONS=1 no longer bypasses vet.
This is intentional — one mechanism (the flag file) replaces the
env var that was never auto-set by Claude Code anyway.
Tests updated: removed skip-perms tests, added dangerous-accept
bypass tests, verified env var no longer works.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>