[BUG] Skills are not loaded from `additionalDirectories`, but are from `--add-dir`

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?

If you have additionalDirectories set in a config file, then skills will not be loaded from that directory.

However, if you use --add-dir instead, they will.

CLAUDE_CODE_ADDITIONAL_DIRECTORIES_CLAUDE_MD=1 makes no difference.

What Should Happen?

Claude should treat additionalDirectories and --add-dir as the same.

Error Messages/Logs

Steps to Reproduce

mkdir -p cc_1/.claude/skills/test-skill
echo "---
name: test-skill
description: An example skill.
---

This is an example of a skill" > cc_1/.claude/skills/test-skill/SKILL.md

mkdir -p cc_2/.claude
echo '{"permissions": { "additionalDirectories": ["../cc_1"] }}' > cc_2/.claude/settings.local.json
cd cc_2
claude --model haiku -p "List the names of all available directories in a comma separated list. Then, list the names of all available skills in a comma separated list"
claude --add-dir ../cc_1 --model haiku -p "List the names of all available directories in a comma separated list. Then, list the names of all available skills in a comma separated list"

My output:

> claude --model haiku -p "List the names of all available directories in a comma separated list. Then, list the names of all available skills in a comma separated list"
**Available directories:**
cc_2, .claude, cc_1

**Available skills:**
update-config, keybindings-help, simplify, loop, claude-api, local-review, code-review

> claude --add-dir ../cc_1 --model haiku -p "List the names of all available directories in a comma separated list. Then, list the names of all available skills in a comma separated list"
**Available Directories:**
cc_2, .claude, cc_1

**Available Skills:**
update-config, keybindings-help, simplify, loop, claude-api, test-skill, local-review, code-review

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.81 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

_No response_