* fix(codex): preserve runtime config without system source
* fix(codex): retain baseline when mirror is skipped
* refactor(codex): extract deprecated hook-flag normalization
Why: codex-config-mirror.ts sat at the 300-line cap, so the missing-source
guard could not land without a max-lines disable.
* fix(codex): bootstrap a baseline when the mirror is skipped
Why: a runtime home seeded outside the mirror (WSL, per-account) never got a
baseline while the source was missing, so promotion stayed inert and silently
reverted the in-Codex change once the source returned.
* fix(codex): stop a synthesized source config from wiping runtime settings
Two routes still reached the #9073 data loss after the missing-source guard:
- Promotion runs before the guard and, with no ~/.codex/config.toml, created
one holding only the promoted keys. The next mirror treated that skeleton as
authoritative and deleted every other runtime setting. It needs no missing
file: `codex mcp add` inside an Orca-launched Codex plus /model was enough to
drop the MCP server for good. Promotion now seeds a brand-new system config
from the runtime's ordinary settings, so the mirror round-trips them.
- A 0-byte source (half-written, or an unhydrated cloud-synced home) still read
as an authoritative empty config and advanced the baseline, making the loss
unrecoverable. A blank source is now treated like a missing one.
Moves the TOML section model out of codex-config-mirror.ts so promotion can
share it without a cycle.
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Co-authored-by: Brennan Benson <79079362+brennanb2025@users.noreply.github.com>
kin001andBrennan Benson
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