tui: ensure TUI plugins load with proper project context when multiple directories are open

Fixes potential plugin resolution issues when switching between projects by wrapping
plugin loading in Instance.provide(). This ensures each plugin resolves dependencies
relative to its correct project directory instead of inheriting context from whatever
instance happened to be active.

Also reorganizes config loading code into focused modules (command.ts, managed.ts,
plugin.ts) to make the codebase easier to maintain and test.

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