Tidied up manual for analysis tools

src/analysis/ClassicalMultiDimensionalScaling.cpp

src/analysis/Commit.cpp

src/analysis/Histogram.cpp

src/generic/DumpAtoms.cpp

src/generic/DumpDerivatives.cpp

src/generic/DumpForces.cpp

src/generic/DumpMassCharge.cpp

src/generic/DumpProjections.cpp

src/generic/Print.cpp

src/generic/UpdateIf.cpp

src/gridtools/ConvertToFES.cpp

src/gridtools/FindContour.cpp

src/gridtools/FindSphericalContour.cpp

src/gridtools/PrintCube.cpp

src/gridtools/PrintGrid.cpp

src/multicolvar/DumpMultiColvar.cpp

src/multicolvar/MultiColvarDensity.cpp

user-doc/Analysis.txt

user-doc/extract