Isolate test root preference persistence

[DemonGiggle]

Summary

• keep production root switching behavior writing the preferred-root marker
• add app/runtime options so tests can switch root dirs without persisting the global preferred root
• update app and web tests to use the non-persisting test app path

Tests

• go test ./...

[gemini-code-assist]

Code Review

This pull request introduces the ability to control whether the preferred root path is persisted when initializing the application or switching runtimes. It refactors the initialization logic by introducing NewAppWithOptions and SwitchRuntimeWithOptions, along with corresponding options structs. The App struct now includes a persistPreferredRoot field to maintain this state. Numerous tests across the codebase have been updated to use these new constructors, and new test cases verify that persistence can be successfully skipped. I have no feedback to provide as there were no review comments to evaluate.