when I contacted Adacore abot this issue, I got the following answer:

  The way you are using gnatstub is correct, and I can confirm that it
  works for AdaCore products. But we cannot say anything for the GNAT versions
  built and distributed outside AdaCore.

Somehow the issue seems specific to the binary distributed in the ubuntu
package.

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https://bugs.launchpad.net/bugs/1738133

Title:
  gnatstub fails to generate any Ada code

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