I have a CLI tool that interacts with Google KMS. In order for it to work, I fetch the user credentials as a JSON file which is stored on disk. Now a new requirement came along. I need to make a web app out of this CLI tool. The web app will be protected via Google Cloud IAP. Question is, how do I run the CLI tool on behalf of the authenticated user?
You don't. Better use a service-account and assign the required role. That service account still could have domain-wide delegation of rights (able to impersonate just any user, which is known).
Running CLI tools from a web-application probably also could/should be avoided. Iit might be better to convert his CLI tool into a Cloud Function and then call it via HTTP trigger, from within the web-application (so that access to the service account is limited as far as possible).
This might also be something to reconsider, security-wise:
Even if it might have been required, with a service-account it wouldn't.