docs(codegen): JSDoc pass over the rest of `src/`

Part of #5368.

JSDoc pass over the remaining files in src/ - generate.ts, generators/, utils/, bin/cli.ts, and codegen.ts.

Includes the minor fix noted in #5368: resolveOperationName in src/generate.ts uses {@linkcode operation.operationId}, which does not resolve because operation is destructured inside the function body.

Blocked on the same tagging-convention question in #5368, and should land after the types.ts pass so the terminology stays consistent.

Fixed by #5374.