Converted gmxpreprocess to compile as C++

Converted gmxpreprocess to compile as C++

Used std:: math function and header, eliminated unused code, vars and
params, used some size_t variables when handling strings.

Added assertions for sqrt operations intended to work on integers that
are perfect squares.

Converted existing assert calls to GMX_ASSERT

Removed include guards from headers

Refactored some ter_db code to be clearer about how generic vs
specific termini are handled.

Made string parameter to _mod into const char *.

Noted TODOs for clean up required for pdb2gmx -merge

Change-Id: Ibe8b8c4b208a39325e6fe450a41d8521daa5d8f0