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>