fix: require explicit opt-in for Engineer plugins

[kaitranntt]

Summary

• make Normal copied skills the recommended/default global Engineer installation
• preserve plugin mode only for explicit persisted plugin consent
• converge missing, malformed, auto, and legacy preferences to Normal skills
• protect multi-kit, Windows legacy-directory, and same-version update paths
• project normal skill runtime paths so packaged skills work outside project CWD

Closes #921

Root cause

The development install pipeline treated historical auto metadata as permission to migrate copied skills into Claude and Codex plugins. Update replayed that value automatically, so users could lose discoverable normal skills without explicitly opting in.

CLI behavior

How should ClaudeKit Engineer be installed?
  Normal skills (recommended)
    Copy to ~/.claude/skills without CK plugins; sync Codex with ck migrate --agent codex
  Claude and Codex plugins (advanced opt-in)
    Register ck provider plugins and preserve this preference for updates

Non-interactive installs choose Normal skills. Existing explicit plugin users remain in plugin mode until they run --install-mode legacy.

Safety

• removes only CK-owned plugin registration/cache state
• preserves user-modified copied files and settings
• resolves consent for secondary Engineer installs before download or mutation
• re-runs global Engineer convergence instead of skipping provider repair at the same version

Validation

• bun run ci:local
• 5,182 CLI tests passed; 65 skipped; 0 failed
• 153 UI tests passed
• typecheck, lint, CLI/UI builds, help parity, generated docs drift passed
• packaged npm tarball and fresh entrypoint verified
• real Engineer skill projected and executed outside project CWD
• independent parallel code review approved

Docs impact

Major. A paired claudekit-docs PR updates English and Vietnamese installation, init, update, doctor, migration, and FAQ pages.

Docs PR: claudekit/claudekit-docs#183