commit-graph: rearrange chunk count logic

The number of chunks in a commit-graph file can change depending on
whether we need the Extra Edges Chunk. We are going to add more optional
chunks, and it will be helpful to rearrange this logic around the chunk
count before doing so.

Specifically, we need to finalize the number of chunks before writing
the commit-graph header. Further, we also need to fill out the chunk
lookup table dynamically and using "num_chunks" as we add optional
chunks is useful for adding optional chunks in the future.

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

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