BitcoinTalk
checkpointing the block chain

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There is no way for the software to automatically know if one chain is better than another except by the greatest proof-of-work.  In the design it was necessary for it to switch to a longer chain no matter how far back it has to go.

The only exception to that is the manual checkpoints I've added.  If it weren't for those, it would be able to reorg all the way back to the first block.
How is the strength of the chain calculated?
Total proof-of-work.