[FEATURE] --bare mode needs a way to load project skills without --add-dir

Preflight Checklist

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

What Should Happen?

--bare mode should have a mechanism to discover and load project skills from .claude/skills/ directories without re-enabling global ~/.claude/CLAUDE.md discovery.

Currently, --bare mode has:

• --plugin-dir for loading plugin skills
• --append-system-prompt-file for loading specific CLAUDE.md files
• --add-dir for adding directories (but this is broken - see below)

It does not have a way to load project-scoped skills from .claude/skills/. The natural approach - --add-dir "$PWD/.claude" - triggers a bug where global ~/.claude/CLAUDE.md is loaded despite --bare (#52267).

Proposed Solution

Either:

1. Fix --add-dir so it doesn't re-enable global CLAUDE.md discovery in --bare mode (#52267), which would make --add-dir "$PWD/.claude" work for both CLAUDE.md and skills discovery, or

1. Add a --skill-dir flag (analogous to --plugin-dir) that points at a directory containing a skills/ subdirectory, or accepts a skills/ directory directly:

``bash
claude --bare --skill-dir "$PWD/.claude/skills"
``

Current Workaround

--plugin-dir happens to work for project skills if pointed at the parent of a skills/ directory:

claude --bare \
  --append-system-prompt-file "$PWD/CLAUDE.md" \
  --plugin-dir "$HOME/.claude/plugins" \
  --plugin-dir "$PWD/.claude"

The second --plugin-dir discovers $PWD/.claude/skills/ and loads them. This works but is non-obvious - --plugin-dir is semantically for plugins, not project skills.

Context

This came up building a --bare mode launcher script that needs to load:

1. A project-specific CLAUDE.md (solved via --append-system-prompt-file)
2. Installed plugin skills like compound-engineering (solved via --plugin-dir ~/.claude/plugins)
3. Project-scoped skills from .claude/skills/ (no clean solution - --add-dir triggers #52267)

Related: #52267 (--bare --add-dir re-enables global CLAUDE.md discovery)

Claude Code Version

2.1.118

Platform

Amazon Bedrock

Operating System

macOS (Darwin 24.6.0)