[BUG] additionalDirectories in settings.json does not trigger discoverability of skill

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?

note: these reported issues appear to be related

• Added support for loading CLAUDE.md files from additional directories specified via --add-dir flag (requires setting CLAUDE_CODE_ADDITIONAL_DIRECTORIES_CLAUDE_MD=1)

-Skills defined in .claude/skills/ within additional directories (--add-dir) are now loaded automatically.

Issue:
additionalDirectories configured in ~/.claude/settings.json under the permissions block does not trigger skill discovery. Skills stored in the specified directories are not discoverable via slash commands when Claude is launched normally.

What Should Happen?

Skills located in .claude/skills/ folders within directories listed under additionalDirectories should be discovered and available as slash commands, identical to the behavior when the same paths are passed via --add-dir at launch.

for example invoking claude like this allows skills in those directories to be discovered as /commands:
claude --add-dir "$PWD\role\dev" --add-dir "$PWD\role\qe"

Error Messages/Logs

No error messages are shown. Skills simply do not appear. Running /status inside the session shows no indication that the additional directories failed to load.

Steps to Reproduce

Add the following to ~/.claude/settings.json:

json{
"permissions": {
"additionalDirectories": [
"C:\\Users\\khurst\\git\\prototypeAutoDiscovery\\role\\dev",
"C:\\Users\\khurst\\git\\prototypeAutoDiscovery\\role\\qe"
]
}
}

Ensure each path contains a .claude/skills/ directory with a valid SKILL.md
Launch Claude normally by typing claude
Attempt to invoke a skill via slash command — it is not discovered
Exit and relaunch using claude --add-dir "C:\Users\khurst\git\prototypeAutoDiscovery\role\dev" --add-dir "C:\Users\khurst\git\prototypeAutoDiscovery\role\qe"
Same skill is now discoverable via slash command

example directory structure
C:\Users\khurst\git\prototypeAutoDiscovery\
├── .claude\
│ ├── commands\
│ ├── skills\
│ └── settings.json
├── role\
│ ├── dev\
│ │ └── .claude\
│ │ ├── commands\
│ │ └── skills\
│ │ └── code-reviewer4\
│ │ └── SKILL.md
│ └── qe\
│ └── .claude\
│ ├── commands\
│ └── skills\
│ └── qe-code-reviewer1\
│ └── SKILL.md
└── src\
└── Main.java

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.91

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

IntelliJ IDEA terminal

Additional Information

at its core, I should be able to structure discoverable skills within a directory structure that I define and point claude to where those skills are so that the skills function as if they were in the anthropic default location. my understanding is that add-dir handles this when put into either the users porject --> settings.json or global --> settings.json and niether one worked for me

here is an example when invoked at startup
PS C:\Users\khurst\git\prototypeAutoDiscovery> claude --add-dir "$PWD\role\dev" --add-dir "$PWD\role\qe"
▐▛███▜▌ Claude Code v2.1.91
▝▜█████▛▘ Opus 4.6 (1M context) with high effort · Claude Team
▘▘ ▝▝ ~\git\prototypeAutoDiscovery

↑ Install the PyCharm plugin from the JetBrains Marketplace: https://docs.claude.com/s/claude-code-jetbrains

❯ /qe
─────────────────────────────────────────────────────────────────────────────────────────────
skills show up, they are discoverable
/qe-code-review2 Perform comprehensive, framework-aware code review of test automation changes (API/UI/E2E). Analyzes project type (Spring Boot, Cypress, Legacy Java, etc.) and applies appropriate best practices. Out…
/qe-code-review4 Perform comprehensive, framework-aware code review of test automation changes (API/UI/E2E). Analyzes project type (Spring Boot, Cypress, Legacy Java, etc.) and applies appropriate best practices. Out…

when I embed this into project--> settings.json. it does not work
{
"permissions": {
"additionalDirectories": [
"C:\\Users\\<user>\\git\\prototypeAutoDiscovery\\role\\dev",
"C:\\Users\\<user>\\git\\prototypeAutoDiscovery\\role\\qe"
]
}
}