Instead of using the `khiter_t`, `git_strmap_iter` and `khint_t` types,
simply use `size_t` instead. This decouples code from the khash stuff
and makes it possible to move the khash includes into the implementation
files.

Next to including several files, our "common.h" header also declares
various macros which are then used throughout the project. As such, we
have to make sure to always include this file first in all
implementation files. Otherwise, we might encounter problems or even
silent behavioural differences due to macros or defines not being
defined as they should be. So in fact, our header and implementation
files should make sure to always include "common.h" first.

This commit does so by establishing a common include pattern. Header
files inside of "src" will now always include "common.h" as its first
other file, separated by a newline from all the other includes to make
it stand out as special. There are two cases for the implementation
files. If they do have a matching header file, they will always include
this one first, leading to "common.h" being transitively included as
first file. If they do not have a matching header file, they instead
include "common.h" as first file themselves.

This fixes the outlined problems and will become our standard practice
for header and source files inside of the "src/" from now on.

The config is not owned by the transaction, so please don’t free it.

This makes the API for commiting or discarding changes the same as for
references.

Transaction.c did not include the visibility definition of its symbol
(that are in git2/transaction.h) and so was by default hidden.

Without this change, compiling with gcc and pedantic generates warning:
ISO C does not allow extra ‘;’ outside of a function.