I added a few tabs to the html manual:
Getting Started
Tutorials
Index of Actions

Fixes #70

internal molfile plugins are now contained in PLMD namespace

No "extern C" in molfile plugins

I fixed a bug occurring when using replicas with different
Hamiltonians (either lamdba dynamics or plumed -hrex branch).
The acceptance was wrong when using a CV that depends on charges
or masses (if charges or masses were changed in the Hamiltonian,
respectively).

related to #113

Closes #113

(no C linkage).

This reverts commit 69728b72.

added "plumed_" prefix to some global functions.
Hopefully fixes #110

I would like @tonigi to have a look at it before merging!

Now all the types and functions declared in the
local version of molfile plugins are properly wrapped
in a namespace.

Possibly fixes #110

(thanks to @OndrejMarsalek)

In commit 606b65a4
I wrote that error was due to user typing "make install"
without "make". I now realized that the error was always there
when PLUMED was installed. I modify the CHANGELOG to make
it more clear. I will also send a patch on the mailing list.

(cherry picked from commit ab739533)

Before this fix, attempting to "make install" without "make" first
could result in corrupted path in the Plumed.inc/Plumed.cmake
files (the one used to patch MD codes). This resulted in linking
errors when trying to use "plumed patch --shared"

These tests were not correctly fixed after the change in component
name from sss/zzz to spath/zpath in Gareth's path variables.