[BUG] Skills from `additionalDirectories` (settings.json) are not loaded

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Skills defined in .claude/skills/ within directories listed under additionalDirectories in settings.json are not loaded into the session. The same directories added via the --add-dir CLI flag work correctly.

Steps to Reproduce

1. Add a directory containing .claude/skills/ to ~/.claude/settings.json:

``json
{
"permissions": {
"additionalDirectories": [
"/path/to/your/project-with-skills"
]
}
}
``

1. Start a Claude Code session normally (claude)
2. Run /context — Skills section shows only built-in skills (e.g. 237 tokens)
3. Run the same session with --add-dir instead:

``bash
claude --add-dir "/path/to/your/project-with-skills"
``

1. Run /context again — all skills from the directory are now loaded

Expected Behavior

additionalDirectories in settings.json should behave identically to --add-dir for skill loading, since it is the persistent equivalent of that flag.

Actual Behavior

Skills are not loaded when the directory is specified via additionalDirectories in settings.json. Only file access works — the directory is accessible for reading/editing, but .claude/skills/ are ignored.

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.74 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

The documentation states:

Skills defined in .claude/skills/ within directories added via --add-dir are loaded automatically and picked up by live change detection.

It only mentions --add-dir and does not clarify whether additionalDirectories in settings provides the same behavior. Based on testing, it does not.

Workaround: Use --add-dir CLI flag explicitly instead of relying on additionalDirectories in settings.