[DOCS] Permissions docs incorrectly state bypassPermissions skips all permission checks

Documentation Type

Incorrect/outdated documentation

Documentation Location

https://code.claude.com/docs/en/permissions

Section/Topic

bypassPermissions mode description and warning block

Current Documentation

The permissions page states:

bypassPermissions | Skips all permission prompts (requires safe environment, see warning below)

And the warning block says:

bypassPermissions mode disables all permission checks. Only use this in isolated environments like containers or VMs where Claude Code cannot cause damage.

What's Wrong or Missing?

Changelog v2.1.78 fixed .git, .claude, and other protected directories being writable without a prompt in bypassPermissions mode. This means bypassPermissions now retains permission prompts for protected directories.

The documentation says bypassPermissions "skips all permission prompts" and "disables all permission checks," which is no longer accurate. Protected directories (.git, .claude, etc.) still require a prompt even in bypassPermissions mode. The current wording would lead users to believe no prompts will appear, which is incorrect.

Suggested Improvement

Update the bypassPermissions description and warning to reflect the protected directory exception:

Before:

bypassPermissions | Skips all permission prompts

After:

bypassPermissions | Skips most permission prompts. Protected directories (.git, .claude, etc.) still require confirmation.

Update the warning block similarly to note the exception.

Impact

Medium - Makes feature difficult to understand

Additional Context

Affected Pages:

| Page | Context |
|------|---------|
| https://code.claude.com/docs/en/permissions | bypassPermissions mode description and warning block |
| https://code.claude.com/docs/en/settings | May reference bypassPermissions in settings descriptions |

Total scope: 2 pages affected

Source: Changelog v2.1.78

Fixed .git, .claude, and other protected directories being writable without a prompt in bypassPermissions mode