bug: ag init --yes does not create config.yaml when .aegis dir has partial state

[OneStepAt4time]

Bug Report

Aegis version: v0.6.7-preview.1

Reproduction

1. Have a ~/.aegis/ directory with some files (e.g., keys.json, state.json) but no config.yaml
2. Run ag init --yes

Expected

Creates config.yaml and prints working next steps.

Actual

⚠️  .aegis/config.yaml already exists.
⚠️  Existing auth token will be preserved.
✅ Using existing .aegis/config.yaml
✅ Reusing existing API token

But config.yaml was never actually created. The command lies about the state.

Impact

MEDIUM — confusing for users recovering from partial/corrupted state. The CLI claims success but the server cannot start (no config).

Related

• bug: ag init generates auth token that running server doesn't accept #3342 — auth token sync issue
• feat: reduce install friction — target 2-command setup (npx + ag run) #3181 — install friction

[OneStepAt4time]

Docs workaround documented in PR #3387. This needs a CLI code fix — when .aegis/ has partial state (e.g. keys.json but no config.yaml), ag init --yes should still write a complete config. Tagging for backend assignment.

[aegis-gh-agent]

Resolved by PR #3391 (merged on 2026-05-14).