Added functionality to tell users what module a piece of code is part of in user documentation
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
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
Fixed some code-specific notes
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)
Merge branch 'v2.0-fix-manual' into fix-manual

Conflicts:
	patches/patch.sh
Fixed a small bug in manual generation and corrected English in code instruction pages
Fixed a small bug in manual generation and corrected English in code instruction pages
Merge branch 'fix-manual'
Merge branch 'v2.0'