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wrangler types --check ignores --env-interface, -c, and other flags, always comparing against default output #13508

@kotkoroid

Description

@kotkoroid

What versions & operating system are you using?

System:
OS: macOS 26.3.1
CPU: (8) arm64 Apple M2
Memory: 129.31 MB / 16.00 GB
Shell: 5.9 - /bin/zsh
Binaries:
Node: 22.14.0 - /Users/johndoe/.nvm/versions/node/v22.14.0/bin/node
Yarn: 1.22.22 - /Users/johndoe/.nvm/versions/node/v22.14.0/bin/yarn
npm: 10.9.2 - /Users/johndoe/.nvm/versions/node/v22.14.0/bin/npm
pnpm: 10.10.0 - /Users/johndoe/.nvm/versions/node/v22.14.0/bin/pnpm
bun: 1.3.12 - /Users/johndoe/.bun/bin/bun
Deno: 2.2.6 - /Users/johndoe/.deno/bin/deno

Please provide a link to a minimal reproduction

https://github.com/kotkoroid/wrangler-types-check-bug

Describe the Bug

wrangler types --check ignores all additional flags (--env-interface, -c, --include-runtime) and always compares the existing worker-configuration.d.ts against what plain wrangler types (with no flags) would generate. This means --check always fails when custom flags are used during generation, even immediately after a fresh wrangler types run.

Please provide any relevant error logs

No response

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