[BUG] global tool permissions are still hobbled

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: .99
• Operating System: macOS
• Terminal: iTerm2

Bug Description

as per issue #925 , the newer versions (after .92) are ignoring global settings in ~/.claude/settings.json. also others have said project permissions are ignored, but I haven't tested this explicitly. Problem is it seems to work initially, but when you relaunch Claude, it's back to disallowing everything.

It just looks like the global config is being silently ignored, based on a background process that's doing .... something. And changing versions forward or backward often, but not always, lets permissions work again, but just once. Sometimes I wonder if it relates to the background loading of MCP's, like if it loaded them, then it won't obey permissions, but if you run your command really fast after startup, maybe it's more likely to work... but then I also tried removing all MCP's and it still failed.

Steps to Reproduce

1. upgrade the version
2. try running a tool that was allowed in ~/.claude/settings.json . I say "try running ls".
3. it probably works without asking for permission
4. exit claude, and enter again
5. try running the tool again
6. it will ask for permission again

Expected Behavior

obey my permissions that I set globally

Actual Behavior

always asking for permission to run 'ls' type commands, which is ridiculous

Additional Context

this is making Claude feel unusable again, as I have to babysit it every 20 seconds rather than having it run for 15 minutes unattended.