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fyi, I was running into this bug as well, but we just upgraded and did not run into it. I think we're avoiding the issue by using DENO_NO_PACKAGE_JSON=true and --node-modules-dir=false (we also run deno in a tmpdir).
Can you try those out and see if they work for you?
Trying to run this with a deno version higher than 1.44 gives the following error
Downgrading to deno 1.44 solves the issue
Looks like a similar issue - https://answers.netlify.com/t/netlify-cli-fails-to-build-edge-functions-locally-with-deno-v1-45-0/121900/5
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