Few doc comments

[dkfellows]

You have not many doc comments. Though there's some other comments that could probably be repurposed. (Doxygen-style comments are a little finicky, but putting API documentation in your header files is a very good idea.)

I recommend putting brief descriptions (@brief) in header files (together with the likes of @param and @return) but leaving detailed descriptions (@details) for the .cpp files where you do the implementations. That seems to produce the best results overall.

For example, in PCC_Writer.h (no @return because there's no result value):

/*! 
 * @brief Write out the structure after the program has computed its contents.
 * @param new_cells_design Structure to write out
 */
void PCC_Writer(CellsDesign &new_cells_design);

In PCC_Writer.cpp:

/**
 * @details
 * Read PCC Writer specifications from the writer.ini file and output of the
 * current configuration to the screen and .log file.
 */
void PCC_Writer(CellsDesign &new_cells_design) {
    ....