Global Agents Inheritance Broken in Project Context

Bug Description
Title: Global agents not visible in project - v1.0.80 regression

Description:

Environment:

• Claude Code version: 1.0.80
• OS: macOS
• Platform: Darwin 24.5.0

Issue:
Global agents from ~/.claude/agents/ are not visible/accessible within project context, despite being properly configured.

Expected Behavior:
Global agents should be available across all projects unless explicitly overridden by project-specific agent configuration.

Actual Behavior:

• Global agents show as "⚠ overridden by projectSettings" in agent list
• No project agents are actually defined
• Phantom .claude/settings.local.json appears to block global agent inheritance

Steps to Reproduce:

1. Have global agents in ~/.claude/agents/ (12 agents configured)
2. Navigate to project directory
3. Run Claude Code
4. Agents are not accessible and show override warning

Additional Context:

• Global agents work correctly outside of project directories
• Issue appears to be related to project settings inheritance in recent version
• Temporary .claude/ folder with settings.local.json was created automatically but contained no agent configuration
• Removing .claude/ folder doesn't resolve the issue permanently

Configuration Files:

• Global agents: ~/.claude/agents/ ✅ (12 files)
• Project settings: .claude/settings.local.json (phantom file)
• User settings: ~/.claude/settings.json ✅

Environment Info

• Platform: darwin
• Terminal: iTerm.app
• Version: 1.0.80
• Feedback ID: 3183b929-1982-4369-8b78-138bb784bd12

Errors

[{"error":"Error: Tool mcp__sequential-thinking__sequentialthinking not found\n    at djB (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1981:4944)\n    at OR (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:330:19859)\n    at rb (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:42835)\n    at ab (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:38356)\n    at Uj (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:38284)\n    at pR (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:38138)\n    at kK (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:35201)\n    at x8 (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:330:4841)\n    at O3 (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:32446)\n    at A.Q.updateContainer (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:336:1837)","timestamp":"2025-08-14T09:28:53.908Z"},{"error":"Error: Tool mcp__sequential-thinking__sequentialthinking not found\n    at djB (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1981:4944)\n    at OR (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:330:19859)\n    at rb (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:42835)\n    at ab (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:38356)\n    at Uj (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:38284)\n    at pR (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:38138)\n    at kK (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:35201)\n    at x8 (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:330:4841)\n    at O3 (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:32446)\n    at A.Q.updateContainer (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:336:1837)","timestamp":"2025-08-14T09:28:53.912Z"},{"error":"Error: Tool mcp__sequential-thinking__sequentialthinking not found\n    at djB (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:1981:4944)\n    at OR (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:330:19859)\n    at rb (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:42835)\n    at ab (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:38356)\n    at Uj (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:38284)\n    at pR (file:///Users/ser/.nvm/versions/node/v22.17.0/lib/node_modules/@anthropic-ai/claude-code/cli.js:332:38138)\n  

Note: Error logs were truncated.