Updating repositories does not trigger necessary actions
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Issue body
This is a behavior seen while using Rockcraft.
Updating repositories entries does not remove PPA files from the disk and does not trigger pull steps.
rockcraft.yaml
```yaml
name: python-3.8
summary: Python 3.8
license: Apache-2.0
description: |
Python 3.8
version: "3.8"
base: ubuntu:22.04
platforms:
amd64:
package-repositories:
- type: apt
ppa: dqlite/dev
priority: always
- type: apt
ppa: deadsnakes/ppa
priority: always
parts:
python:
plugin: nil
stage-packages:
- python3.8
```
Performing pull step:
```bash
rockcraft pull --shell-after
Launching instance...
Retrieved base ubuntu:22.04 for amd64
Extracted ubuntu:22.04
Package repositories installed
Executed: pull pebble
Executed: pull python
Launching shell on build environment...
root@rockcraft-keystone-53910271:~/project# ls -alh /etc/apt/sources.list.d/
total 4.0K
drwxr-xr-x 2 root root 4 Apr 3 13:09 .
drwxr-xr-x 8 root root 9 Apr 26 2022 ..
-rw-r--r-- 1 root root 164 Apr 3 13:09 snapcraft-ppa-deadsnakes_ppa.sources
-rw-r--r-- 1 root root 160 Apr 3 13:09 snapcraft-ppa-dqlite_dev.sources
root@rockcraft-keystone-53910271:~/project#
```
Then, removing the `deadsnakes/ppa` PPA:
```diff
diff rockcraft.yaml/before rockcraft.yaml/after
16,18d15
< - type: apt
< ppa: deadsnakes/ppa
< priority: always
```
This is the result:
```bash
rockcraft pull --shell-after
Launching instance...
Retrieved base ubuntu:22.04 for amd64
Extracted ubuntu:22.04
Package repositories installed
Executed: skip pull pebble (already ran)
Executed: skip pull python (already ran)
Launching shell on build environment...
root@rockcraft-keystone-53910271:~/project# ls -alh /etc/apt/sources.list.d/
total 4.0K
drwxr-xr-x 2 root root 4 Apr 3 13:09 .
drwxr-xr-x 8 root root 9 Apr 26 2022 ..
-rw-r--r-- 1 root root 164 Apr 3 13:09 snapcraft-ppa-deadsnakes_ppa.sources
-rw-r--r-- 1 root root 160 Apr 3 13:09 snapcraft-ppa-dqlite_dev.sources
```
The sources file is not removed, and the pull stage is not retriggered. (this should have failed)
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