For extension development, reloading now rebuilds the full chat history
so updated component rendering is visible immediately, not just in new
messages.
Also removes broken test for deleted chalk-logger.ts extension (npm
dependency resolution is already covered by with-deps test).
When a user edits settings.json while pi is running (e.g., adding
enabledModels), those settings would be lost when pi saved other
changes (e.g., changing thinking level via Shift+Tab).
The fix re-reads the file before saving and merges the current file
contents with in-memory changes, so external edits are preserved.
Adds test coverage for SettingsManager.
ferologics