Changed manual after discussions about issue #97

I split up the section on the input syntax and rewrote the introductions
to plumed and to collective variables in general
Changed Quick Introduction to Getting Started
move Intro to collective variables. Getting Started instead of Quick Intro
Fixed some typos in manual
Fixed reference to multicolvar in colvar introduction
Merge branch 'issue-97'
Fixed some bugs in documentation

There are now fewer warnings when Doxygen runs