The per-root merge in _copy_dist_payload treated the first level under
skills/ as the replace unit, but skills live at skills/<category>/<skill>.
A distribution shipping one skill inside a category rmtree'd the whole
category directory, wiping every skill the user (or hermes update) had
placed there — the exact scenario of issue #25120 that this PR claims to
fix. A shipped directory with no files of its own is now a container:
its children are merged one level down, and the replace unit becomes the
nearest directory that holds a file (a skill dir always holds SKILL.md).
A symlinked category (skills/devops -> shared dir) is a container too,
so the pre-write symlink check now covers it instead of silently
unlinking the link and dropping the shipped copy in its place.
Review finding: categorised skill payload rmtree'd skills/<category>/,
destroying sibling user and bundled skills; symlinked category was
unlinked rather than refused.
fa915784cb