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A fresh, isolated CLAUDE_CONFIG_DIR (used to keep an injected API key away from a stored claude.ai OAuth login) looks like a brand-new Claude Code profile to the CLI, so it replays its ENTIRE first-run sequence on every single launch: the theme picker, the security-notes screen, the per-project "trust this folder?" dialog, and (running with --dangerously-skip-permissions) a one-time bypass-permissions warning — confirmed live, none of which a real, already-onboarded profile shows again. - New registry-declared env-kind field `skipFirstRunPrompts` (alongside apiKeyTrustFile, which it reuses) — claude's entry only, carried through buildCustomModelInjection (pure) into applyCustomModelInjection (IO). - seedFirstRunOnboardingState(): merges hasCompletedOnboarding: true and this session's own projects[workingDir].hasTrustDialogAccepted: true into the same <configDir>/.claude.json the API-key trust file already writes to — other projects and other fields on this session's own entry are left untouched. - seedSkipBypassPermissionsPrompt(): merges skipDangerousModePermissionPrompt: true into <configDir>/settings.json, a separate file, same corrupt-tolerant merge behavior. - applyCustomModelInjection() gains an optional workingDir parameter, threaded from session.workingDir (dedicated apply route) / resolvedCasePath (quick-start route) — boot recovery omits it (a dialog already answered once needs no re-seed on the same, persisted isolated directory). Tests added at the pure-builder, IO-wrapper (including merge-preserves- other-fields and corrupt-file-tolerance cases), and existing directory- listing assertions updated for the new settings.json file. Typecheck/ lint/format clean; full suite shows no new regressions (baseline pre-existing Windows-environment failures unchanged, 8 more passing tests than before — the ones added here). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01RqZeHrRS6DYcGcGX2p9EwG