stage filter not applied to overlay content
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### Bug Description
During the `STAGE` step, content from the overlay is migrated to the stage directory. The stage filter is not applied to this content.
In the case of organizing content to the overlay, files from this layer cannot be filtered because:
- using the `overlay` filter on the part will be ineffective (executed **before** the content is organized to the overlay)
- using the `overlay` filter on a following part will remove the file from the **following** part's layer, still staging the one from the initial part.
Now that `(overlay)` is a valid identifier to target the overlay, use it in the `stage` filter to prefix files to include/exclude.
### To Reproduce
`python3 -mcraft_parts --partitions default --overlay-base /tmp/overlay --trace -v prime`
### part yaml
```shell
parts:
rootfs:
plugin: nil
override-build: |
echo "a" > $CRAFT_PART_INSTALL/a
echo "b" > $CRAFT_PART_INSTALL/b
organize:
'*': (overlay)/
stage:
- (overlay)/a
```
### Relevant log output
```shell
N/A
```
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