paper: Minor changes and extra TODOs
mpi/flow: Remove copy_kind block to avoid nested timing blocks

Nested timing blocks were already invalid, and will soon be
completely broken by PAPI support.
Add PAPI hardware performance counter support

PAPI support must be enabled by changing the PAPI_MAX define in
thread.cpp, after which the set of counters can be controlled at
startup time with the PENTAGO_PAPI environment variable.