additionalDirectories setting does not grant Read tool access to files outside project

Bug Description

The additionalDirectories setting in .claude/settings.local.json does not grant the Read tool access to files in the specified directories. Files outside the project directory remain blocked with EPERM: operation not permitted even after being added.

Steps to Reproduce

1. Add a directory outside the project to additionalDirectories (either via /add-dir command or manually in settings):

``json
{
"permissions": {
"additionalDirectories": [
"/Users/<user>/Documents/Screenshots/"
]
}
}
``

1. Attempt to read a file from that directory using the Read tool
2. Observe EPERM: operation not permitted error

Observed Behavior

• Read tool: EPERM: operation not permitted
• Bash with ls -la: Works (can stat the file, see metadata/permissions/size)
• Bash with cp: Operation not permitted (even with dangerouslyDisableSandbox: true)

This suggests the sandbox allows stat() but blocks open() for file reads in additionalDirectories paths.

Expected Behavior

After adding a directory via additionalDirectories, the Read tool (and Bash file operations) should be able to access files in that directory.

Environment

• Claude Code version: 2.1.59
• OS: macOS (Darwin 25.3.0)
• macOS Full Disk Access: Granted to terminal app
• Setting location: .claude/settings.local.json (project-level)

Notes

• The /add-dir command confirms the directory was added: Added /Users/<user>/Documents/Screenshots/ as a working directory and saved to local settings
• The directory in question (~/Documents) is macOS TCC-protected, but Full Disk Access is already granted to the terminal application
• This may be a sandbox profile issue where additionalDirectories paths are not being included in the sandbox allow-list for file reads