repository: fix free problem with repo_clear(the_repository)

the_repository is special. One of the special things about it is that it does not allocate a new index_state object like submodules but points to the global the_index variable instead. As a global variable, the_index cannot be free()'d. Add an exception for this in repo_clear(). In the future perhaps we would be able to allocate the_repository's index on heap too. Then we can revert this. the_repository->index remains pointed to a clean the_index even after repo_clear() so that it could still be used next time (e.g. in a crazy use case where a dev switches repo in the same process). Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com> Signed-off-by: Junio C Hamano <gitster@pobox.com>