crane: deleted files persist in crane export output

[alexey-igrychev]

Describe the bug

When using crane export to export an image from a registry, deleted files are not ignored despite being removed during the build process.

To Reproduce

1. Create a Dockerfile with the following commands:

   FROM alpine:3.12
   RUN mkdir -p test
   RUN echo "Hello World" > /test/hello.txt
   RUN rm -rf /test
   RUN mkdir -p /test
   RUN echo "Hello World" > /test/hello2.txt

2. Start a local registry:

   docker run -d --name=registry --restart=always -e REGISTRY_STORAGE_DELETE_ENABLED=true -p 5000:5000 registry

3. Build the Docker image:

   docker build -t localhost:5000/test .

4. Push the image to the local registry:

   docker push localhost:5000/test

5. Export the image using crane and check for files in the test directory:

   crane export localhost:5000/test - | tar -ztv | grep "test/"
   
   -rw-r--r--  0 0      0          12 Oct 29 22:12 test/hello2.txt
   -rw-r--r--  0 0      0          12 Oct 29 21:45 test/hello.txt

6. Compare with Docker's export behavior:

   docker run --name test localhost:5000/test
   docker export test | tar -ztv | grep "test/"
   
   drwxr-xr-x  0 0      0           0 Oct 29 22:12 test/
   -rw-r--r--  0 0      0          12 Oct 29 22:12 test/hello2.txt

Expected behavior

crane export should ignore deleted files, consistent with Docker's export behavior.

Additional context

• Output of crane version: v0.20.2
• Registry used (e.g., GCR, ECR, Quay): Local registry on localhost:5000

[alexey-igrychev]

The same issue with crane flatten command:

$ crane flatten localhost:5000/test --tag localhost:5000/test:flatten                                  
2024/10/29 22:32:01 pushed blob: sha256:2c695611fb1e094624385a8e6f26d9617ea095d295fd879088569f69b48e983c
2024/10/29 22:32:01 existing blob: sha256:2c695611fb1e094624385a8e6f26d9617ea095d295fd879088569f69b48e983c
2024/10/29 22:32:01 pushed blob: sha256:472616afd54c24f0d61cd3dd307cae5ae24aaf2b14a527db49bd38bfd8b9c4e5
2024/10/29 22:32:01 localhost:5001/test:flatten: digest: sha256:19b2ab1c17df3c87b88235dc6b54b6f53766801cb56f0a8a3d65361dea25a096 size: 428
localhost:5001/test@sha256:19b2ab1c17df3c87b88235dc6b54b6f53766801cb56f0a8a3d65361dea25a096

$ crane export localhost:5000/test:flatten - | tar -ztv | grep "test/"
-rw-r--r--  0 0      0          12 Oct 29 22:12 test/hello2.txt
-rw-r--r--  0 0      0          12 Oct 29 21:45 test/hello.txt

[nabokihms]

@imjasonh hello! I think we can fix this but firstly need your approval.