Fixed dependencies

Plumed.inc and Plumed.cmake are now regenerated each time.

(cherry picked from commit cff6770749e1bbe027460e1a1c9e3d98a45c4f69)
typo
Fixed header
Reference to published paper

Plumed paper has now a volume and page
Improved doc

I removed one page (WhatsNew) and merged it in the changelog page for
2.0
Improved doc for DISTANCE
Improved doc for ANGLE
Added info option in patching script

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 a273bb84d5e9e9b953eace77a2d149b0e8a13add)
Added -q option to patch

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 7152d46f43f7322dc9a365fceaf8c455ea85564c)

Conflicts:
	patches/patch.sh
Fixed some code-specific notes

(cherry picked from commit e1d01e84e34673c42fc149c62766570ab391c68b)
Fixed a small bug in manual generation and corrected English in code instruction pages
Fixed a bug in Read that used to appear when you tried to use periodic variables
Updated changelog

(cherry picked from commit 2c272e4abdfbb01f513fd8ef1cb0855cbe5a4b4f)
Added warning for namd and virial
Fix in backup output files

(thanks to Toni Giorgino)

I fixed a missing include.

Original comment:
Fixes in backup output files - cant rename open file under windows - print reason for failure - remove leak of FILE*s

(cherry picked from commit 448e84fcfdd0a8f6996a8e6f3307444fc45f6497)
Addresses #63 (warning only)
Typo
Support for explicit include files

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

Closes #69
Improved makefile

Needed to have proper regeneration of links when new .h files are added.
I also added several comments.
Updated developer Doxyfile to latest doxygen version