autoUpdates: false is not honoured on native installs — version pin silently reverted

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report
• [x] I am using the latest version of Claude Code (2.1.235)

What's Wrong?

"autoUpdates": false in the user config is not honoured by the native installer path.
The CLI updated itself anyway, silently reverting a deliberate version pin.

I had pinned to 2.1.233 by repointing the claude symlink in order to bisect a bug
across versions. At the next launch the update ran regardless:

{"timestamp":"2026-08-19T02:19:34.818Z","path":"native","outcome":"success",
 "version_from":"2.1.233","version_to":"2.1.235"}

The config also contains "autoUpdatesProtectedForNative": true, which may be relevant
to why the user-facing setting is being ignored on this install path.

Expected Behavior

With "autoUpdates": false set, the CLI should not update itself. If the setting is
deliberately not supported for native installs, it should say so — warn at startup, or
reject the setting — rather than accepting it and silently doing the opposite.

Steps to Reproduce

1. Native install (~/.local/share/claude/versions/, symlinked into ~/.local/bin).
2. Set "autoUpdates": false in the user config.
3. Pin an older version by repointing the claude symlink.
4. Launch. The version is silently updated to latest; the pin is gone.

Workaround

DISABLE_AUTOUPDATER=1 in the environment does hold the pin. Only the env var works;
the config setting does not.

Why this matters beyond the setting itself

It makes version-sensitive debugging unreliable. I hit this while bisecting a
reproducible OOM across 2.1.233/234/235 (#88029) — without the env var, the binary changes
underneath the experiment and results are attributed to the wrong version. The first
pass of that investigation wrongly suspected a 2.1.235 regression for exactly this
reason.

Environment

| | |
|---|---|
| Version | 2.1.235 (updated from 2.1.233 against the setting) |
| Install method | native |
| OS | WSL2 Ubuntu 24.04, kernel 6.18.33.1-microsoft-standard |
| WSL | 2.7.8.0 |
| Windows | 11, build 10.0.26200.9168 |