[Bug]: Settings saves revert external edits to settings.json #18571

Before submitting

• I searched existing issues and did not find a duplicate.
• I included enough detail to reproduce or investigate the problem.

Area

apps/server

Steps to reproduce

1. Run t3 serve and connect a client.
2. Make the client save settings faster than every 100 ms, or save once within 100 ms after the next step.
3. Replace settings.json from outside T3 Code, for example with a script that adds a customModels entry and renames the new file into place.
4. Read settings.json again.

Expected behavior

The save applies its patch to the file on disk. The external edit stays.

Actual behavior

The save writes the server's cached settings back, and the external edit is gone.

Cause:

• updateAndPersistSettings (apps/server/src/serverSettings.ts) applies the patch to the cached settings and writes the whole result.
• The cache refreshes only through the file watcher, debounced to 100 ms of quiet (Stream.debounce).
• Every save also triggers a watcher event. Saves that arrive less than 100 ms apart keep the debounce from firing, so the cache never reloads and every save writes the old file back.

We hit this with saves 20 to 40 ms apart from the client loop in #18572. A fleet script's edit to settings.json was reverted about 20 seconds after it landed.

A related case: once the watcher has loaded a settings.json that does not parse, the cache holds defaults. The next save then writes defaults plus the patch over the user's file, although the loader says such a file "must stay on disk for the user to repair".

Impact

Major degradation or frequent failure

Version or commit

0.0.46-nightly.20261010.2935 (98beed1). Same code on origin/main f498b35.

Environment

t3 serve on macOS and Linux.

Workaround

After an external edit, wait until settings.json has stopped changing, then read it back and apply the edit again if it was reverted.