[BUG] permissions.additionalDirectories does not load skills from added directories (--add-dir CLI flag does)

Description

Skills defined in .claude/skills/ within additional directories are not loaded when configured via permissions.additionalDirectories in settings, but are loaded when using the --add-dir CLI flag.

The settings documentation states that permissions.additionalDirectories is functionally equivalent to --add-dir, and the skills documentation says:

Skills defined in .claude/skills/ within directories added via --add-dir are loaded automatically

Steps to Reproduce

Setup

Additional directory structure:

.local_skill/
  .claude/
    skills/
      my-skill/
        SKILL.md   # valid frontmatter + content

Case 1: settings file (FAILS)

.claude/settings.local.json:

{
  "permissions": {
    "additionalDirectories": ["../.local_skill"]
  }
}

Launch: claude

• The directory IS recognized as an additional working directory (shown in environment info)
• Skills are NOT listed in the system message skill list
• /my-skill returns "Unknown skill"

Case 2: CLI flag (WORKS)

Launch: claude --add-dir ../.local_skill

• Skills ARE listed in the system message skill list
• /my-skill works correctly

Expected Behavior

Both methods should load skills identically, as documented.

Environment

• Claude Code version: 2.1.63
• OS: macOS (Darwin 23.6.0)