More C++ standardization

[dbanks12]

clang-tidy+clang-format+clangd can't fix everything for us. We should do a manual scan and standardize:

1. struct and array initialization
2. auto
3. references
4. namespaces
5. includes done
6. index/init.hpp
7. all pointer/malloc usage in c_bind args/returns

[dbanks12]

Replaces:

1. Standardize struct and array initialization aztec3-circuits#215
2. Standardize usage of auto aztec3-circuits#219
3. Standardize usage of references aztec3-circuits#220
4. Standardize usage of namespaces & includes aztec3-circuits#190
5. Standardize usage of index/init.hpp aztec3-circuits#221
6. Standardize all pointer/malloc usage in c_bind args/returns aztec3-circuits#206