`primed-stage-packages` isn't in manifest.yaml when using override-prime
Metadata
Current evaluation
No evaluation has been recorded for this issue yet.
Issue body
### Bug Description
When using `override-prime`, the `primed-stage-packages` entry in the `manifest.yaml` is never populated.
This is due to an upstream issue in craft-parts (https://github.com/canonical/craft-parts/issues/1122).
We've worked around this problem before by warning when `override-prime` is used (https://github.com/canonical/snapcraft/issues/4547).
### To Reproduce
Build the snap below with `SNAPCRAFT_BUILD_INFO=y snapcraft` and inspect the manifest with and without the `override-prime` keyword.
### Environment
Snapcraft 8.9.0
This affects core22+ since this is a craft-parts issue.
### snapcraft.yaml
```yaml
name: my-snap-test
version: '0.1'
summary: A test snap to demonstrate primed-stage-packages
description: |
This is a simple snap to show how stage-packages are primed.
grade: stable
confinement: strict
base: core22
parts:
my-part:
plugin: nil
stage-packages:
- curl
override-prime: |
craftctl default
```
### Relevant log output
```shell
n/a
```
### Additional context
_No response_
Evaluation history
No evaluation history available.