fix(3663): applySurface creates missing dest dirs (Codex P1-1)

Remove the fs.existsSync(dest) guard in applySurface so _syncGsdDir is
always called. _syncGsdDir already does mkdirSync(..., { recursive: true })
so the destination is created when absent — recovering partially-initialized
or user-deleted runtime config dirs. Also threads manifest through to
_syncGsdDir as optional 4th arg (used by P1-2 Hermes fix).

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