- Add PackageSource type for npm/git sources with optional filtering
- Migrate npm:/git: sources from extensions to packages array
- Add getPackages(), setPackages(), setProjectPackages() methods
- Update package-manager to resolve from packages array
- Support selective loading: extensions, skills, prompts, themes per package
- Update pi list to show packages
- Add migration tests for settings
closes#645
When 429/500 errors occur during tool execution, empty assistant messages
with stopReason='error' get persisted. These break the tool_use -> tool_result
chain for Claude/Gemini APIs.
Added centralized filtering in transformMessages to skip assistant messages
with empty content and no tool calls. Provider-level filters remain for
defense-in-depth.
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.
