EPERM: Cannot read/write project-level .claude/ files from outside project directory

Bug Report

Environment

• Model: Claude Opus 4.5 (claude-opus-4-5-20251101)
• Platform: macOS (Darwin 25.3.0)
• Date: 2025-01-25

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Description

When Claude Code is launched from a directory other than the project root (e.g. ~/), it scans and reports errors from project-level .claude/ directories (e.g. ~/Documents/GitHub/project/.claude/), but cannot read or write files in those directories due to EPERM: operation not permitted.

Reproduction

1. Have a project at ~/Documents/GitHub/project/ with a .claude/ directory containing settings.json and agents/*.md
2. Launch Claude Code from ~/ (home directory)
3. Claude Code reports parse/validation errors for files inside the project's .claude/ directory
4. Attempting to read or edit those files returns EPERM: operation not permitted

Observed Behavior

• Claude Code scans project-level .claude/ directories on startup
• Reports errors (missing frontmatter, invalid schema, etc.)
• Cannot actually access the files to fix or even read them
• User is shown errors they cannot resolve within the current session

Expected Behavior

Either:

1. Claude Code should have read/write access to .claude/ directories it scans and reports errors for, or
2. Claude Code should not scan/report errors for .claude/ directories it cannot access, or
3. The error output should clearly indicate that the file is outside the current session's permission scope

Related

• See also #20699 (multiple bugs including settings schema validation and agent frontmatter issues)