Claude Code claims permission denied despite --dangerously-skip-permissions

[davidguttman]

Environment

• nightshift: v0.3.4
• claude: 2.1.77
• OS: Arch Linux x86_64

Problem

Tasks are failing because Claude Code reports 'permission denials' even though:

1. dangerouslyskippermissions: true is set in config
2. nightshift passes --dangerously-skip-permissions flag (confirmed via source)
3. Manual invocation works: claude --print --dangerously-skip-permissions 'create file, git branch, commit' succeeds

Evidence

From nightshift logs:

The implementation summary acknowledges this failure ('permission denials') but the task requirements are unmet
...
No branch was created, no files were modified
...
The submission is a permission request, not an implementation

files_modified: 0 on every iteration despite Claude running for 10-30 minutes per task.

What works

• forty.news project succeeded (has explicit .claude/settings.local.json with permissions.allow list)
• Manual claude invocation with same flags works for git operations

Suspicion

Either:

1. Claude's project-level .claude/settings.local.json overrides the --dangerously-skip-permissions flag
2. Something about the non-interactive/--print mode + long tasks causes permission prompts mid-execution that block
3. The prompt/task structure causes Claude to self-report blocked state without actually trying

Config

providers:
  claude:
    enabled: true
    datapath: ~/.claude
    model: sonnet
    dangerouslyskippermissions: true

[marcus]

Hey @davidguttman! Starling here (AI assistant on the project). 👋

Thanks for the detailed report — the diagnostic work here is really solid. You've got a clear reproduction gap (forty.news works, others don't), and your suspicion about the cause is worth testing first.

Most likely culprit: project-level .claude/settings.local.json overriding the flag

Claude Code respects a precedence order: .claude/settings.local.json > .claude/settings.json > CLI flags (in some configurations). If the failing repos have a .claude/settings.local.json that sets restrictive permissions, it can override --dangerously-skip-permissions — which would explain exactly why forty.news works (it has an explicit allowlist) while others don't.

Quick check:

1. Run find <failing-repo> -name 'settings.local.json' -path '*/.claude/*' to see if that file exists
2. If it does, check whether it has a permissions.deny or restrictive permissions.allow list

Workaround to test: Add the same permissions.allow list to the failing repos' .claude/settings.local.json (or delete the file entirely if it's not intentional) and see if nightshift can proceed.

Flagging this for Marcus to dig into — if it is a settings.local.json precedence issue, we may want nightshift to either warn about it in the logs or document it more prominently. ✦