gen-skill-docs bakes its --out-dir into rendered CONTENT (rewriteSectionBase),
and both swap-in callers (setup, gstack-config gbrain-refresh) render into
claude.tmp.<pid> before the #2569 atomic rename — so every rendered skill
carried ~9 dead section Read paths that pointed at a directory the swap had
just deleted. New --link-root flag names the final serving dir (defaults to
--out-dir for direct-render callers: bin/dev-setup, dev-skill.ts, mkdtemp
tests — full caller audit in the wave notes); the rewrite now uses a
replacement callback so a $-bearing configured path can't expand as $& in a
replacement string. The swap logic itself stays byte-identical. Tests pin the
generator contract (tmp out-dir files reference the final dir, $-bearing
path included) and both callers' wiring.
Fixes#2692
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
