Remove (part of) underscore-prefixed C++ symbols.

Remove (part of) underscore-prefixed C++ symbols.

This commit is mostly the result of (using GNU sed syntax)
  sed -i -re 's/\<_([a-zA-Z]+)\>/\1_/g'
on the affected files. Some additional manual renaming was done.
optionsassigner.cpp was manually edited a bit more to update comments
and to remove unnecessary use of bit flags.
Also added a few 'explicit' keywords to constructors.

selection/ and trajectoryanalysis/ directories still contain a lot of
these, but this commit is large enough as it stands.

Change-Id: I7f4bf42ec5d9d762fefcff289e38b6b6b231b82b