I allowed include commands such as #include "../module/file.h",
only in the case where module is an used module (or the current module).

Later I would like to see if it is possible to eliminate
the "make links" stuff completely.

maketools/cppcheck has been renamed into maketools/codecheck

To use it:
make cppcheck only runs cppcheck
make plumedcheck only runs plumedcheck
make codecheck runs both and aggregate messages (to be used e.g. on travis)

Needed to have proper regeneration of links when new .h files are added.
I also added several comments.

Instead of using links to other source directories
we now use explicit include files. The approach is more
robust.

Closes #69

One can now produce a Makefile.conf and a sourceme.sh
using autoconf. Just type:

./configure

Or maybe

./configure CXX=icpc

In case you want to use mpi, just use:

./configure CXX=mpic++

Everything should be smooth. I took care that the generated Makefile.conf
is compatible with those stored in configurations/. In this way,
one can always resort to a saved configuration file. Moreover,
jumping between git branches (without need of reconfiguring) will be
easier.

More info on the manual page (no need to use autoconf to compile
the manual and see that page)

Closes #46

I use a lot "make install" to keep different installed
versions so as to compare them. In this way I do not
have to cd everytime.

I think I fixed the problem that sometime leads to errors
in builds with a lot of cpus (make -j 12)

There was a problem if starting compilation in some directory.
Now also the links to other directories are generated recursively,
thus are by construction up to date for all the used modules.

Notice that config/ and wrapper/ are treated as special cases

Now the file containing the configuration options is a .cpp file.
This limits the effect of the change in the configuration to
a single object file and remove the need for BUILDAFTER variable
in Makefiles

error in cleaning is now ignored

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