Update and simplify tooling

[Preston12321]

• The old diffing script isn't necessary when we're no longer generating per-shard bundles. Delete it.
• The add roots script refers to logs and shards. Generalize it to take a destination directory, meanwhile fixing a usage text issue and tweaking a couple other bits of output.
• Since we're the no longer tracking CCADB roots in this repository, the script that builds our PEM bundles needs to be updated. Do that. The updated script spits out a production bundle by default, or a testing bundle if --testing is supplied. It also takes an --output file that defaults to ./bundle.pem.
• The pull roots script has to be updated every time we deploy a new log or shard, because it's trying to pull every single log shard every time. Instead, change it to download only a single log (shard), with the log URL being given by the user. It's easy enough to script a for loop in bash for those who want to use this against multiple logs/shards.

Note: The names of some of these scripts will be a little inaccurate after this change. Don't worry, I've got a PR further up the stack that'll rename them, but I kept them the same here because git's diffing algorithm wasn't picking up the rename and made the change harder to review.