--project-dir fails to find metadata.yaml when running in destructive mode
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### Bug Description
This is a low priority bug, but I thought I'd report it anyway.
In this project: https://code.launchpad.net/~ubuntu-release/autopkgtest-cloud/+git/autopkgtest-cloud/+ref/master
Our CI recently started failing, with no apparent reason.
The charmcraft version is 3.1.1
Part of our ci is the following command:
```
charmcraft pack -v --destructive-mode -p charms/focal/autopkgtest-cloud-worker/
```
which has been failing with:
```
:: :: + /snap/charmcraft/4369/bin/python3 -I /snap/charmcraft/4369/lib/python3.10/site-packages/charmcraft/parts/reactive.py autopkgtest-cloud-worker /build/lpci/project/parts/charm/build /build/lpci/project/parts/charm/install
:: :: FATAL: No bundle.yaml (Bundle) or metadata.yaml (Charm) found, cannot proof
:: :: charm tool execution command=['charm', 'proof']
```
However, the metadata.yaml is there, as the following works:
```
cd charms/focal/autopkgtest-cloud-worker/
charmcraft pack -v --destructive-mode
```
FTR, we have a pretty outdated charm. We don't have a charmcraft.yaml and instead have a metadata.yaml, layer.yaml, etc, and I'm aware we're building our charms in this pipeline in a pretty janky way :)
### To Reproduce
git clone -b master https://git.launchpad.net/autopkgtest-cloud
cd autopkgtest-cloud/
snap install lpci --classic
lpci run # feel free to comment out the other jobs in .launchpad.yaml to make it faster
### Environment
destructive mode via LPCI
focal
### charmcraft.yaml
```shell
the yaml files are under:
charms/focal/autopkgtest-cloud-worker/
charms/focal/autopkgtest-web/
```
### Relevant log output
```shell
:: :: + /snap/charmcraft/4369/bin/python3 -I /snap/charmcraft/4369/lib/python3.10/site-packages/charmcraft/parts/reactive.py autopkgtest-cloud-worker /build/lpci/project/parts/charm/build /build/lpci/project/parts/charm/install
:: :: FATAL: No bundle.yaml (Bundle) or metadata.yaml (Charm) found, cannot proof
:: :: charm tool execution command=['charm', 'proof']
```
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