Charles_Gibbs:
Where can I find a manual for the Arduino code not just bits and peices but the whole manual maybe in PDF?
I don't think there is such a manual.
Arduinos are programmed with standard C++ code
All of the standard Arduino specific features such as digitalWrite() are documented in Reference pages of this website.
Documentation for the features in additional libraries depends on the author of the library and, unfortunately, many Open Source programmers are not interested in, or are not good at, writing documentation.
...R