Is blanket write protection on ~/.claude/ directory intentional?

Question

Edit and Write tools are in my global settings.json allow list:

"allow": [
  "Read",
  "Write",
  "Edit",
  ...
]

However, any Edit or Write operation targeting files under ~/.claude/ triggers a permission prompt regardless. This applies to all files in the directory, not just settings files — for example, writing to ~/.claude/scripts/log-rule-access (a user-created helper script) also prompts.

Is this intentional? If so, it would be helpful to document it. If it's specifically protecting settings/hooks files, the current implementation is broader than necessary since it also blocks writes to user scripts and other non-sensitive files under ~/.claude/.

Environment

• Claude Code on macOS (Darwin 25.3.0)
• Permission mode: Ask (also observed in dangerous/bypass mode)