[BUG] System overwrite ~/.claude/settings.json

Environment

• Platform (select one): Anthropic MAX
• Claude CLI version: 1.0.35
• Operating System: e.g. macOS 14.4.1
• Terminal: mac terminal 2.14

Bug Description

Adding new user-level /permission erases existing content in ~/.claude/settings.json

Steps to Reproduce

1. Manually add settings.json
2. add new user permission within CLI

Expected Behavior

Appending new permissions

Actual Behavior

Overwriting permissions

Additional Context

In 1.0.35, whether adding manually or through the CLI, claude doesn't seem to recognize or remember permissions: settings.json makes no apparent difference at a user level. This feels like a new bug -- hasn't been a problem in the past. Seems tied to a system crash that wiped all my settings and config files during update to 1.0.35. Also noticing what seems like unusual 'forgetfulness' wrt user-level Claude.md file, but that may be confirmation bias.