t2000: consolidate second scenario into a single test block

t2000: consolidate second scenario into a single test block

The second test scenario in t2000 consists of several fragmented
test_expect_success blocks that handle data setup, tree writes,
execution of git-checkout-index, and final state validation.

Consolidate these nine separate blocks into a single self-contained
test block. This follows the modern Git testing standard where setup,
execution, and validation of a single logical scenario are kept
together.

As a result of this consolidation, the show_files() helper and its
associated test_debug calls are no longer used and have been removed.
This also removes a dependency on the non-portable 'find -ls' command.

Helped-by: Karthik Nayak <karthik.188@gmail.com>
Helped-by: Junio C Hamano <gitster@pobox.com>
Signed-off-by: Zakariyah Ali <zakariyahali100@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>