`--setting-sources user` does not suppress project-level skill discovery

Summary

--setting-sources user is expected to limit config loading to user-level sources (~/.claude/), but project-level skills from .claude/skills/ directories are still discovered and loaded at session start.

Reproduction

1. Have a project with skills in .claude/skills/ at multiple directory levels
2. Launch Claude Code with --setting-sources user
3. Observe that project skills are still loaded:

``
Loaded 1 skill from <project>/.claude/skills
Loaded 2 skills from <project>/sub/.claude/skills
Loaded 3 skills from <project>/sub/deeper/.claude/skills
``

Expected behavior

With --setting-sources user, no project-level configuration should be loaded — including skills.

Actual behavior

Project-level skills are discovered and loaded regardless of the flag.

Environment

• macOS (Darwin 25.2.0)
• Alias: alias claude="claude --setting-sources user"