S3 URI validated as regular directory on copy or move

\Drupal::service('file_system')->copy('private://my-folder/my-file.txt', 's3://my-bucket/my-file.txt');

Did you include the actual bucket name here ? If so that would be incorrect use of the Drupal S3FS StreamWrapper. For us s3:// is defined as being “the root of the configured bucket plus any configured sub path prefix” (this is different than if you have previously worked with the AWSSDK directly where you need to include the bucket name on each access).

Should do it check for the existence of the bucket/directory on the remote S3 service instead?

The s3fs_file table is considered and authoritative cache of the bucket status and is required to be kept up to date if making changes outside of the s3fs module (see README). While we call the internal decorated method, that method relies on standard PHP functions which are handled by the S3fsStream::class that routes back to the checking the s3fs_file table.

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