chunk-format: restore duplicate chunk checks

Before refactoring into the chunk-format API, the commit-graph parsing
logic included checks for duplicate chunks. It is unlikely that we would
desire a chunk-based file format that allows duplicate chunk IDs in the
table of contents, so add duplicate checks into
read_table_of_contents().

Signed-off-by: Derrick Stolee <dstolee@microsoft.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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