lapack and blas README files were not shown.

I guess this happened with some doxygen update that ignores README files.
Solved renaming to README.md.

[makedoc]

to doxygen 1.8.7

I also re-imported lapack and blas

I removed many graphs that were probably not useful
and were cluttering the output. Moreover, I
enabled the search engine and added an alphabetic
list of classes (classes -> class index)

It was wasting space (especially the developer one) and anyway improperly
formatted. Could be readded later if we fix formatting.

Changed Doxygen options so that full source is included. Source 
files are also easier to be navigated in the browser now.

All the source code have been moved into subdirectories of src/
Some of these subdirectories are treated in a special manner:
src/wrapper contains the wrappers for MD codes
src/main contains the main.cpp file
src/config contains files generated without compilation,
  just based on configuration info
src/lib is the place where executables and libraries are put
  at the end
src/cltools contains the command line tools
src/tools contains plumed tools (reusable classes)
src/basic contains PlumedMain, Action hierarchy and other basic stuff
src/multicolvar contains MultiColvar stuff
src/imd is the interactive MD (still not totally portable).

Notice that, to allow easy inclusion of .h files from other modules,
I link all the directories in src/ into module directory. In this
way it is possible e.g. to write #include "config/PlumedConfig.h"

See src/README and src/basic/Makefile to understand how inter-module
dependencies are set

Added a tool for generating template versions of the various collective
variables.  This involved changing the secondary structure variables
work (by default you now do LESS_THAN).  In addition, plumed now understands
that atoms can be specified in multiple ways sometimes.

Also changed the developer manual so as to make it easier to find the
tutorials

This allow avoiding warning (and possibly errors) with parsing
comments inside comments. The pages are not in developer-doc
directory, and a link to them is given in class Colvar, Function,
and CLTool

the header files for these abstract base classes

Doxygen groups

more comprehensible quick intro to the code.  In addition I have added
an extract script much like the one we use for the developer
manual so that we can make lists of the various re-usable tools
that people implement in the code.

I also upgraded the doxygen configuration files to 1.7.4 version

This is the draft version that I prepared and that we will use as
a starting point. Still it is a bit dirty, and I will try to improve
documentation and delete unused routines