Reorganize some of the unwieldly parts of the codebase

* Moved commands into their own folder to reduce `bin.rs`'s size
* Moved all of the VFS-related functionality into its own folder
* Documented a lot of functions, including a few very obscure ones

src/commands/mod.rs

@@ -0,0 +1,5 @@
+mod serve;
+mod init;
+
+pub use self::serve::*;
+pub use self::init::*;