Fix 'make codedoc' for out-of-tree builds.

I was recently starting to use out-of-tree builds to not pollute the source tree with build files and to be able to switch between release and debug builds easily. For example I use from top-level directory: 
```
mkdir debug ; cd debug ; ../configure  --with-no-optimise --enable-debug
```
And to build from top-level:
```
make -C debug
```

Almost everything worked out-of-the-box, but I noticed that `make -C debug codedoc` did not.
This PR fixes it by passing the correct directories to naturaldocs.