Move mutation-related files to a new mutation/ directory. The names
are kept in the global namespace to reduce churn; the names are
unambiguous in any case.
mutation_reader remains in the readers/ module.
mutation_partition_v2.cc was missing from CMakeLists.txt; it's added in this
patch.
This is a step forward towards librarization or modularization of the
source base.
Closes#12788
