Added PDF manual. I had to reorganize a bit the documentation to make
it more linear. In particular, I assigned each of the previously
"dangling" pages as subpage of another one (e.g. DEBUG keyword).
Additionally, I changed a bit the way MD-specific instructions are linked
and added some comment about the PDF manual in the introduction.

The most important change is that I am not using the Layout anymore since
it was difficult to keep it in sync. Now, in the html version, only
the left-side tree is visible, and the tabs disappeared. I don't think
this is a big issue but we might try to solve it.

PDF manual is still a bit buggy: some links are not properly resolved
and images are not shown. I think we can solve these issues later.

Addresses #101

I split up the section on the input syntax and rewrote the introductions
to plumed and to collective variables in general

This commit resolves issue #97  However, I also changed the layout of
the colvar page on the manual so I thought I would push it on a branch
before merging it into master.  Let me know if there are any objections
to the changes I have made.

there where random "@" appearing here and there. Fixed now

"extract" is way faster. Additionally, spaces are better preserved
in the manual (especially in indented input files)

If "plumed" executable is not available, sourceme.sh file is sourced

I updated doxyfile to latest doxygen version. I also
enables the search engine. This required a small fix on the
extract script so that "action" pages receive a proper name
for the index.

Allows to avoid verbose logging. The option is now used in user-doc/extract
to simplify the generation of code-specific notes

(cherry picked from commit 7152d46f)

Conflicts:
	patches/patch.sh

This allows one to create information on the differences in
the various patching procedures by executing:

plumed patch -i

This information is also put into the online manual

(cherry picked from commit a273bb84)

Allows to avoid verbose logging. The option is now used in user-doc/extract
to simplify the generation of code-specific notes

This allows one to create information on the differences in
the various patching procedures by executing:

plumed patch -i

This information is also put into the online manual

Here you can use regex to refer to argument in a list
For example in
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
d1: DISTANCE ATOMS=7,17 COMPONENTS
PRINT ARG=(d1.[xy]|t[0-9]) STRIDE=100 FILE=colvar FMT=%8.4f

Currently the .diff file is compulsory, the .config is not. So, the list
of MD codes should be built looking at .diff files

Webpage with modules is not generated if no modules have been installed

This funcitonality allows you to add tutorials written in Doxygen
and links to external websites.  They are called How Tos though

An output file was not set

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

It could be that this problem was coming from my specific awk version.
Anyway, now it seems more robust.

For otherwise uncategorized actions

Too many files were opened.

more robust and extendible.  Also shifted function creation to
MultiColvar.  This makes ActionWithDistribution more reusable

having

DISTANCE
ANGLE
etc

which each one being a link you have

DISTANCE    calculate the distance between a pair of atoms
ANGLE       calculate the angle between three atoms
etc

each one of DISTANCE, ANGLE and so on is still a link to the more detailed description