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коменты

Избавиться от длинных строчек.
Конструктор можно -нужно сделать так:
Bacteria::Bacteria(Water* water,int x,int y,int energy,const Bacteria* parent)
: water(water)
,x(x)
,y(y)
,energy(energy),
genome(new Genome(this,parent))
,parent(parent)

attack = genome->attack;
birth_time = water->time; эти тоже можно включить по идее

Bacteria::Bacteria(Water* water,int x,int y,int energy,const Bacteria* parent):water(water),x(x),y(y),energy(energy),genome(new Genome(this,parent)),parent(parent)

Коменты)

Почитайте про uint8_t и таких типах, по возможности переведите весь ко на них, те переменные, которые не планируется менять во время работы программы обозначить как constexpr.
int x,y; - можно заменить на std::pair - выглядит лучше
переведите все на умные указатели
Избавьтесь от friend

int cmd;

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