vfs: Use existing type aliases consistently

Makes use of the VirtualDir and VirtualFile aliases across the board
instead of having a few isolated places that don't use it.

src/core/file_sys/nca_patch.h

@@ -106,7 +106,7 @@ public:
 
     bool Resize(std::size_t new_size) override;
 
-    std::shared_ptr<VfsDirectory> GetContainingDirectory() const override;
+    VirtualDir GetContainingDirectory() const override;
 
     bool IsWritable() const override;