Remove unused dependencies

...and move dependencies only used in Workers to `devDependencies`.
They're bundled in with the Worker code, so don't need to be
installed again. Importantly, this change removes `better-sqlite3`,
meaning Miniflare no longer has any native dependencies other than
`workerd`.

Fixes #599

Fixes cloudflare/workers-sdk#3423
Fixes cloudflare/workers-sdk#3449
Fixes cloudflare/workers-sdk#3531
Fixes cloudflare/workers-sdk#3534
Fixes cloudflare/workers-sdk#3708
Fixes cloudflare/workers-sdk#3746

Closes cloudflare/cloudflare-docs#10241