Bug: Claudia incompatible with Claude Code v1.0.7+ centralized file system

[gander]

Problem Description

Claudia is looking for permissions in ./.claude/ but no longer finds them there. The application expects the older directory structure, while Claude Code has migrated to a centralized storage system.

Expected Behavior

Claudia should be compatible with the current Claude Code file system structure (v1.0.7+) where:

• Project settings are stored in ~/.claude/projects/[encoded-directory-path]/
• Global settings are in ~/.claude/settings.json
• Central project permissions are in ~/.claude/.claude.json

Actual Behavior

Claudia continues to search for configuration files in the legacy ./.claude/ directory structure:

project/
├── .claude/
│ ├── settings.json # Project settings
│ ├── settings.local.json # Local preferences
│ └── [permissions] # Local permission configs

This causes the application to fail to find permissions and project configurations.

Environment

• Claude Code version: v1.0.7+ (centralized system)
• Claudia version: Current (expecting legacy structure)
• Migration date: June 2025 (v1.0.7 migration of allowedTools and ignorePatterns)

Additional Information

File System Evolution

Legacy System (pre-v1.0.7):

• Local .claude/ directory in each project
• Project-specific permissions stored locally
• Settings mixed with project files

Current System (v1.0.7+):

• Centralized storage in ~/.claude/projects/[slug]
• Better security isolation (permissions don't enter repos)
• Easier multi-project management
• History preservation when moving directories

Root Cause

The official Claude Code documentation hasn't been updated to reflect these changes, leading to:

• Third-party applications relying on outdated file locations
• Integration problems with existing tools and scripts
• Developer confusion about current file structure

Impact

• Claudia cannot access project permissions and settings
• Users cannot manage Claude Code projects through Claudia
• Application functionality is broken for current Claude Code versions

This issue affects all third-party applications that integrate with Claude Code and haven't been updated for the centralized file system.

[GFTXWD]

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