[makedoc]

I think the inclusion of numpy headers was related to non used variables
forgotten from an intermediate implementation.
I just removed them. In this manner it is not necessary that numpy is
already installed when plumed extension is compiled.

Numpy would be anyway required to run our test.

(@gtribello noticed this is #423)

provided by @tetsuyamorishita

Closes #422

@@tetsuyamorishita please fill the module documentation with some text. Thanks!

@tetsuyamorishita I merged all your commits into a single one.

Notice that I reimplemented the Communicator function that you needed
(Max) together with a few others (Min and Prod).

See #422

As of PLUMED 2.4.1, an error is triggered when aligning using a pdb file
with zeros in the last column. I here fix the provided pdb file.

See this:
https://groups.google.com/d/msgid/plumed-users/4e2f69b8-1b2d-4bd3-a2e3-ecdfeef65d77%40googlegroups.com?utm_medium=email&utm_source=footer

close #380

Closes #354