Modernize src/c* src/d* and src/e* files (#6263)

Modernize src/c* src/d* and src/e* files (#6263)

* Modernize src/c* src/d* and src/e* files

* default operator
* redundant init
* delete default constructors on CraftDefinition childs (never used)
* fix some missing init values
* const ref fix reported by clang-tidy
* ranged-based for loops
* simple conditions & returns
* empty stl function instead of size
* emplace_back stl function instead of push_back + construct temp obj
* auto for some iterators
* code style fixes
* c++ stl headers instead of C stl headers (stdio.h -> cstdio)