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multiple opportunities for developers to permanently cause the loss of user funds. For example, the creation of P2SH-P2WPKH or P2SH-P2WSH addresses requires the strict use of compressed pubkeys, otherwise funds can be irrevocably lost

It may be true in general, but this is not a good example. BIP 32 already introduced strict use of compressed pubkeys, so it’s used by all HD wallets. Dealing with both compressed and uncompressed addresses for the same private key is a major pain. So this restriction should actually prevent bugs.

it is completely reasonable for projects such as the lightning network to reject forming bidirectional payment channels (i.e. a multisignature P2SH address) using non-SW P2SH outputs due to the possibility of malleability

More than “reasonable”, it’s a requirement. Malleabitliy is a key reason why Lightning is still not being used. It’s waiting for SegWit or something similar and it will only work on top of SegWit outputs. I don’t see why this would make fungeability worse than you describe. Transactions that open a channel will be obvious regardless. Until you decide to open a channel, there’s no need to use SegWit outputs, so you can simply “hide” among the regular UTXO set until then.

The discount itself appears to have been determined arbitrarily and not for any scientific or data-backed reasoning.

This may be true for the specific discount, but having a discount by itself increases the incentive to consume, rather than create, UTXOs, which are an expensive resource.

It might be desirable to determine the specific discount using a market mechanism, just as fees are, but this would add enormous complexity. Perhaps it can be done later.

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Bitcoin

Historical Bitcoin Core Client Performance

Historical Bitcoin Core Client Performance

After reading about performance optimizations on the Bitcoin Core blog, I wanted to see a chart of that. I couldn’t find one, so I spun up a bunch of EC2 nodes and set out to measure how long it took each new version of the bitcoin core client to sync the full blockchain.

Initial Blockchain Download (IBD) on Amazon EC2 (~474K blocks, t2.xlarge, 4 cores, 16 GiB, GP2 200 GiB SSD). Light blue is blocks up 2014–01–01, dark blue up to early July 2017. For explanation of Assume Valid Block, see text below.
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Version 0.2 has Linux support, unlike 0.1, so that’s why I picked it. I’ll probably need to compile all the dependencies using old versions of libraries. There’s also Gitian, but I don’t know if that’s available for these old versions.
On the other hand, running on Windows might be less hassle, because it’s easier to install old crappy libraries. However you can’t simply run Windows XP on EC2, it seems like you have to use Windows Server; I don’t know if that causes problems.