fix: prevent /model command from overwriting externally-added settings

[Br1an67]

TLDR

The /model command (and any setValue() call) silently removes entries manually added to settings.json while the app is running. This fix ensures only the changed key is written to disk.

Dive Deeper

Root cause: setValue() called saveSettings(settingsFile), which passed the entire in-memory originalSettings object to updateSettingsFilePreservingFormat(). The merge function (applyUpdates()) iterates over keys in the update object — for array-valued keys (like modelProviders), the stale in-memory version completely replaces the on-disk version, silently dropping entries the user added after app startup.

Fix: Added saveSettingsKey(filePath, key, value) which:

1. Builds a minimal update object containing only the changed key path (e.g., { model: { name: "new-model" } })
2. Passes only this minimal object to updateSettingsFilePreservingFormat()
3. Since applyUpdates() only touches keys present in the update, all other file content is preserved

The existing saveSettings() function is kept for backward compatibility but is no longer called from setValue().

Testing Matrix

• All 87 existing settings tests pass
• All 8 existing commentJson tests pass
• New test: verifies that updating only model.name preserves a modelProviders array on disk

Closes #2454