Phase 3+4: FileTree tools + async backup + DiffMode + integration cleanup

## Phase 3: Missing models
- FileTreeSnapshot (path→hash mapping)
- FileTreeComparer (compare two snapshots)  
- FileTreeDiffer (generate diff for PatchMiddleware)
- StorageManager async wrappers

## Phase 4: Integration cleanup
- Bootstrap uses ResolveExtension to inject BinaryDiffer
- DiffMode (Serial/Parallel) wired into pipeline

Part of GeneralUpdate v2 refactoring plan.