[BUG] Claude code configuration files and folders issue

Environment

• Platform (select one):
• Anthropic API
• Claude CLI version: 1.0.89 (Claude Code)
• Operating System: Linux 6.12.28-1-MANJARO
• Terminal: Native Linux terminal

Bug Description

Inconsistent and confusing configuration directory structure across different installation methods and components.

Steps to Reproduce

1. Install Claude Code (tested with both nvm and native installations)
2. Run Claude Code and observe configuration file locations
3. Attempt to use IDE integration
4. Check where configuration files are created and expected

Expected Behavior

• All Claude Code configuration should be in a single, consistent directory (e.g., ~/.claude/) according to docs
• IDE integration should use the same configuration directory structure
• Installation method should not affect configuration file locations

Actual Behavior

• Main configuration data stored in ~/.claude.json (root of home directory)
• Session data and other config stored in ~/.claude/ directory
• IDE integration expects files in ~/.config/claude/ide/ but Claude Code Extension creates them in ~/.claude/ide/
• Requires manual symlink: ~/.claude/ide → ~/.config/claude/ide for IDE integration to work
• MCP settings, chat history, and other critical data mixed in the root-level JSON file

Additional Context

This creates confusion about where Claude Code stores its data and requires manual intervention (symlinks) for basic functionality like IDE integration to work properly. The configuration should follow a consistent pattern
regardless of installation method.