Fixes #3318.

Document git_fetch_options struct and fix typo.

git_fetch_options was missing from the API docs because it lacked a
documentation comment above the struct declaration.
I used the git_checkout_options docstring as a template.

Also fixes a typo in git_remote_prune_refs (remote, not reamote).

Fix macro redefinition warning

List a submodule only once when the path matches a submodule in the index

examples: modernise the fetch example

The header src/cc-compat.h defines portable format specifiers PRIuZ, PRIdZ, and PRIxZ. The original report highlighted the need to use these specifiers in examples/network/fetch.c.  For this commit, I checked all C source and header files not in deps/ and transitioned to the appropriate format specifier where appropriate.