Pack file verification

Add a checkout example

While the aim of libgit2 was to conform to C90 code, we never instructed
the compiler to enforce C90 compliance. Thus, quite a few violations
were able to get into our code base, which have been removed with the
previous commits. As we are now able to build libgit2 with C90 enforced,
we can set the C_STANDARD property for our own build targets.

Note that we explicitly avoid setting the C standard for our third-party
dependencies. At least the zlib target does not build with C90 enforced,
and we do not want to fix them by deviating from upstream. Thus we
simply enforce no standard for them.

While we want to enforce strict C90 mode, this may cause issues with
system provided header files which are themselves not strictly
conforming. E.g. if a system header has C++ style comments, a compiler
in strict C90 mode would produce an error and abort the build. As the
user most likely doesn't want to change the system header, this would
completely break the build on such systems. One example of this is
mbedtls, which provides such header files.

The problem can be worked around by distinguishing between
system-provided and project-provided include directories. When adding
include directories via "-isystem" instead of "-I", the compiler will
skip certain checks and print out less warnings. To use system includes,
we can simply add the "SYSTEM" flag to CMake's `INCLUDE_DIRECTORIES` and
`TARGET_INCLUDE_DIRECTORIES` functions. Note that we have to split the
include directories into two variables because of this, as we definitely
still want to check for all warnings produced by our own header files.

C++ style comment ("//") are not specified by the ISO C90 standard and
thus do not conform to it. While libgit2 aims to conform to C90, we did
not enforce it until now, which is why quite a lot of these
non-conforming comments have snuck into our codebase. Do a tree-wide
conversion of all C++ style comments to the supported C style comments
to allow us enforcing strict C90 compliance in a later commit.

We strive to keep an options structure to many functions to be able to
extend options in the future without breaking the API. `git_indexer_new`
doesn't have one right now, but we want to be able to add an option
for enabling strict packfile verification.

Add a new `git_indexer_options` structure and adjust callers to use
that.