Clarify Cloudflare target deployment and extension footguns

[elithrar]

While building a real Flue Worker, a few Cloudflare target docs points were easy to misread and led to avoidable backtracking.

• Deploy with the generated config: dist/<worker>/wrangler.json, not the source-root wrangler.jsonc.
• Add a wrangler deploy --dry-run --config dist/<worker>/wrangler.json step before deploy.
• Make it clearer that Flue generates FLUE_* bindings; users only declare migrations for those classes.
• Clarify when scheduleEvery(...) belongs in cloudflare = extend(...) instead of a Worker cron handler.
• Warn against direct run(...) calls from app routes, email handlers, or schedulers when users want workflow run history.
• Point users at the mounted workflow route, or shared pure helper modules, for app-owned ingress.