Update documentation and makefile for submodules

* We now check to make sure that the required files are on disk and show an error message if not found.
* README updated to indicate that submodule initialisation is needed.

Sample output when the module can't be found:

```
Meterpreter's submodule dependencies can't be found.
From your git console, please run:
  $ git submodule init && git submodule update
```
This one's for you @todb-r7 :)