repository: initialize index in `repo_init()`

When Git starts, one of the first things it will do is to call
`initialize_the_repository()`. This function sets up both the global
`the_repository` and `the_index` variables as required. Part of that
setup is also to set `the_repository.index = &the_index` so that the
index can be accessed via the repository.

When calling `repo_init()` on a repository though we set the complete
struct to all-zeroes, which will also cause us to unset the `index`
pointer. And as we don't re-initialize the index in that function, we
will end up with a `NULL` pointer here.

This has been fine until now becaues this function is only used to
create a new repository. git-init(1) does not access the index at all
after initializing the repository, whereas git-checkout(1) only uses
`the_index` directly. We are about to remove `the_index` though, which
will uncover this partially-initialized repository structure.

Refactor the code and create a common `initialize_repository()` function
that gets called from `repo_init()` and `initialize_the_repository()`.
This function sets up both the repository and the index as required.
Like this, we can easily special-case when `repo_init()` gets called
with `the_repository`.

Signed-off-by: Patrick Steinhardt <ps@pks.im>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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