cppcheck warnings

Especially when printing size_t it is better to use << operator
which always uses the right size.

This commit contains changes automatically generated by plumedbot on Travis-ci.

This commit contains changes automatically generated by plumedbot on Travis-ci.

- dumpgrid
- pca
- mds

Using auto when creating a unique_ptr

Notice that this change required a bit of hacking.
setAveragingAction now takes a std::unique_ptr as an argument.

I think ownership is clearer now since it is explicitly declared.

Notice that files are closed on destructor anyway.

I went through cppcheck warnings (style) and fixes those I understood.
Mostly issues related to scope of variables.

Not complete yet

Made landmarkRegister return a unique_ptr

Regenerated after c40b96fe

[makedoc]

After \par Examples there should be an empty line

[makedoc]