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

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

Using auto when creating a unique_ptr

I removed the remaining delete statements.

Notice that in order to make this change I had to change a bit the interface
of a few functions. The difficulty here is that there are parts of the
code storing a reference to a std::vector of pointers and those are affected
when the vector is transformed into a vector of unique_ptr.

Notice that files are closed on destructor anyway.

This is a huge commit, applying indentation to the whole
code. Notice that this commit is made on master branch
after having merged with -s ours from branch v2.3

See #215

Also tidied up how STRIDE and USE_ALL_DATA works for analysis
objects.  Now everything works in a manner similar to GRID

[makedoc]