Replace `std::cerr` outputs with functions in `main.cpp`

[adisidev]

Currently main.cpp is very clustered due to the heavy usage of std::cerr for output messages. Often times we log every time we use a function. For example, write functions are almost always preceeded by a print statement with "Writing to ". We should just embed these messages in the functions themselves, as smaller chunks are easier to understand.

[adisidev]

Same with error handling.

[adisidev]

Duplicated #172