fix: pin json-schema-to-zod to zodVersion 3 in generator

The Publish to npm workflow failed on commit 0667413 because
json-schema-to-zod@2.8.1 defaults to generating Zod v4-style code
(z.core.$ZodIssue), but this project depends on zod@^3.25.28.
Passing zodVersion: 3 explicitly and regenerating tools.ts fixes the
tsc build.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>