Added 'documentation' target to master Makefile.

Builds the html documentation
Added QM parts to master Makefile.

It is not included in the target 'all', because that is the default
target and would fail if you didn't have rdkit set up.

i.e. you have to run `$ make all QM` to actually make everything including 
the QM stuff.
Added QM installation instructions.
Fix the QM parts of the master Makefile

Now the bin/symmetry target actually installs it, and the 'eg2' target
runs the QM target (which is now required, as this example runs with QMthermo)
Remove unused import statements
Moved cclib into external (and updated import statements accordingly).

`import cclib`
becomes
`import external.cclib as cclib`
(or probably could have done `from external import cclib`)