redundant whiteouts cause a path error
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Issue body
## Problem
When building an image where new packages are added (either via `stage-packages` or `overlay-packages`), the corresponding OCI layer will flag some of the underlying part's files to be whiteout.
Not only this is redundant (because the introduction and deletion of the package files happen within the same part/layer), but it also causes a path error to some tools (like `dive`).
In short, whiteout should only be used to flag **files from underlying layers** for deletion, but not files from the same layer.
## How to reproduce
rockcraft.yaml:
```
name: hello
version: "1.0"
base: ubuntu:20.04
parts:
hello:
plugin: nil
stage-packages:
- hello
```
Then:
```
$ rockcraft pack
...
$ skopeo copy oci-archive:hello_1.0.rock docker-daemon:test-image:latest
$ dive test-image:latest
Image Source: docker://test-image:latest
Fetching image... (this can take a while for large images)
Analyzing image...
Building cache...
path error at layer index Index(0:1): unable to remove '/usr/bin/hello.dpkg-new': path does not exist: /usr/bin/hello.dpkg-new
path error at layer index Index(0:1): unable to remove '/usr/share/doc/hello.dpkg-new': path does not exist: /usr/share/doc/hello.dpkg-new
path error at layer index Index(0:1): unable to remove '/usr/share/doc/hello/changelog.Debian.gz.dpkg-new': path does not exist: /usr/share/doc/hello/changelog.Debian.gz.dpkg-new
path error at layer index Index(0:1): unable to remove '/usr/share/doc/hello/copyright.dpkg-new': path does not exist: /usr/share/doc/hello/copyright.dpkg-new
path error at layer index Index(0:1): unable to remove '/usr/share/info/hello.info.gz.dpkg-new': path does not exist: /usr/share/info/hello.info.gz.dpkg-new
path error at layer index Index(0:1): unable to remove '/var/cache/apt/archives/hello_2.10-2ubuntu2_amd64.deb': path does not exist: /var/cache/apt/archives/hello_2.10-2ubuntu2_amd64.deb
path error at layer index Index(0:1): unable to remove '/var/lib/apt/extended_states.1NJeQR': path does not exist: /var/lib/apt/extended_states.1NJeQR
path error at layer index Index(0:1): unable to remove '/var/lib/apt/extended_states.3b7RY9': path does not exist: /var/lib/apt/extended_states.3b7RY9
path error at layer index Index(0:1): unable to remove '/var/lib/dpkg/status-new': path does not exist: /var/lib/dpkg/status-new
path error at layer index Index(0:1): unable to remove '/var/lib/dpkg/tmp.ci': path does not exist: /var/lib/dpkg/tmp.ci
path error at layer index Index(0:1): unable to remove '/var/lib/dpkg/info/hello.list-new': path does not exist: /var/lib/dpkg/info/hello.list-new
file tree has path errors
```
### Origin of the problem
The new layer created by the rockcraft part has all of the whiteout files listed in the `dive` error above. This can be confirmed by:
```
$ skopeo copy oci-archive:hello_1.0.rock oci:test-image
$ ls -l test-image/blobs/sha256/
total 33824
-rw-r--r-- 1 cris cris 508 Apr 25 10:12 8a023a80af56db32c245ed2fb0a542eb44ceabc24695abcf26a9d9a8095689a3
-rw-r--r-- 1 cris cris 6033508 Apr 25 10:12 8a9350d62b7b6564badccbd007a354a6eab0ddf7aeb1006b5692e179d2e244e8
-rw-r--r-- 1 cris cris 28565998 Apr 25 10:12 8e5c1b329fe39c318c0d49821b339fb94a215c5dc0a2898c8030b5a4d091bcba
-rw-r--r-- 1 cris cris 734 Apr 25 10:12 e41e5ca3f81a4dadba93d0fd71f2ee8c3ef693620933b65b0d325fb490162370
$
$ tar tf test-image/blobs/sha256/8a9350d62b7b6564badccbd007a354a6eab0ddf7aeb1006b5692e179d2e244e8 | grep wh
./var/cache/apt/archives/.wh.hello_2.10-2ubuntu2_amd64.deb
./var/lib/dpkg/.wh.status-new
./var/lib/dpkg/.wh.tmp.ci
./var/lib/dpkg/info/.wh.hello.list-new
./var/lib/apt/.wh.extended_states.3b7RY9
./var/lib/apt/.wh.extended_states.1NJeQR
./usr/bin/.wh.hello.dpkg-new
./usr/share/doc/.wh.hello.dpkg-new
./usr/share/doc/hello/.wh..wh..opq
./usr/share/doc/hello/.wh.changelog.Debian.gz.dpkg-new
./usr/share/doc/hello/.wh.copyright.dpkg-new
./usr/share/info/.wh.hello.info.gz.dpkg-new
```
These whiteout files do not exist in layer 8e5c1b329fe39c318c0d49821b339fb94a215c5dc0a2898c8030b5a4d091bcba, and thus the whiteout is redundant.
Evaluation history
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