[FEATURE] Support CLAUDE.md inside .claude/ folder for better organization

Preflight Checklist

• [x] I have searched existing requests and this feature hasn't been requested yet
• [x] This is a single feature request (not multiple features)

Problem Statement

Currently, project instructions must be placed in CLAUDE.md at the project root, while all other Claude Code configurations are stored in the .claude/ folder:

project/
├── CLAUDE.md ← Project instructions (root)
└── .claude/
├── settings.json ← Settings
├── commands/ ← Custom slash commands
└── skills/ ← Skills

Feature request:

It would be cleaner to support CLAUDE.md inside the .claude/ folder, allowing all Claude Code configurations to be centralized in one place:

project/
└── .claude/
├── CLAUDE.md ← Project instructions (proposed)
├── settings.json
├── commands/
└── skills/

Benefits:

• Cleaner project root (less clutter)
• All Claude Code configs in one place
• Easier to manage/backup Claude Code settings
• Consistent with how other tools organize their config (e.g., .vscode/, .github/)

Proposed Solution

Suggestion:

• Support both locations for backward compatibility
• Priority: .claude/CLAUDE.md > ./CLAUDE.md (or configurable)

Alternative Solutions

_No response_

Priority

Critical - Blocking my work

Feature Category

CLI commands and flags

Use Case Example

_No response_

Additional Context

_No response_