[BUG] Onboarding Process Ignores Environment Settings.

Environment

• Platform (select one):
• [ ] Anthropic API
• [ ] AWS Bedrock
• [*] Google Vertex AI
• [*] Other: LLM Gateway
• Claude CLI version: 1.0.60 & 1.0.61
• Operating System: MacOs 15.5
• Terminal: Various. ZSH, Bash

Bug Description

Claude Code ignores the settings in ~/.claude/settings.json (or even configurations in the environment) if the .claude.json file doesn't exist, or exists but does not have the hasCompletedOnboarding option set to true. Claude Code will attempt to do the onboarding, but will force the user to create a console or subscription account to complete the onboarding. For enterprise users who needs to go through an LLMGateway you cannot complete the onboarding with out adding the required entry in the appropriate line in the .claude.json file by hand.

Steps to Reproduce

1. Setup Authentication for LLMGateway in settings.json or in environment variables.
2. Delete the .claude.json file.
3. You now cannot fix your claude code setup until you recreate the .claude.json file with the hasCompletedOnboarding option set to true.

Expected Behavior

This is a regression. When setting up Claude Code in mid July I was able to bypass the Console Vs Subscription question by having a API Key and URI in my Environment.

Actual Behavior

You must edit your .claude.json file by hand to skip onboarding to be able to utilize an LLMGateway.

Additional Context