fix(init): keep user files in legacy command folders (#1874)

* fix(init): keep user files in legacy command folders

Legacy cleanup removed each pre-skills tool's <tool>/commands/openspec/ folder recursively whenever it existed, deleting any command the user kept there along with OpenSpec's three files. init runs that cleanup unprompted when there is no TTY, so agents and CI lost those files without --force.

Directory entries now name the files OpenSpec wrote there. Cleanup deletes only those, removes the folder only once nothing else is left in it, and reports each entry it kept. A folder holding none of OpenSpec's files is no longer treated as legacy, and a folder holding only them is removed exactly as before.

* docs: drop legacy migration-guide edit from legacy cleanup fix

docs/ is legacy; the canonical docs-lab page (help/legacy/migration.md) is
still a skeleton, so there is nothing to update there yet.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* fix(init): recognize legacy command files by their OpenSpec markers

Legacy cleanup treated any regular file named proposal/apply/archive in a
<tool>/commands/openspec/ folder as OpenSpec's, so a user-authored file
with one of those names, including one swapped in while the upgrade prompt
waited, was still deleted.

Every legacy slash command was generated with the OpenSpec markers, and
OpenSpec refused to update one without them. A file now counts as
OpenSpec's only when its content still carries them, and cleanup checks
that again immediately before each unlink. A symlinked command folder is
never followed. Test fixtures now use marker-wrapped content like the real
generated files.

Closes #1873

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* fix(init): recheck each legacy command file before the directory cleanup deletes it

The directory cleanup loop classified a folder's managed files once and then
unlinked every one of them. A file the user swapped in after that scan was
deleted and reported as deleted. Each file is now checked for the OpenSpec
markers immediately before its unlink; a file that fails the check is kept
and reported as kept.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

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Co-authored-by: Clay Good <hi@claygood.com>
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>