Issue 4550 (1/2) Avoid "using namespace std;" in included files

Issue 4550 (1/2) Avoid "using namespace std;" in included files

These are manual changes in preparation for an automated removal of
"using namespace std;".

Mostly these are additions of using-declarations for commonly used
types and containers (e.g. std::string, std::vector) to *.cc files so
that they will continue to build after the big removal.