skaffold dependency cache is incorrect after host before hooks run and are sent to docker API

If you use `useDockerCLI: false` you cannot have before hooks that move/delete files that your Dockerfile needs. We currently use a before hook to copy in generated protobuf code into a Go container and that's how we discovered this issue. I have made a dummy repo that replicates this issue very simply here: https://github.com/SophisticaSean/skaffold-docker-hook-bug

Simply toggling `useDockerCLI` off and on showcases the issue. With the `useDockerCLI` enabled there's no way for us to pass file dependency information to the docker CLI so this issue is not present. If you disable file dependency caching by changing [this line](https://github.com/GoogleContainerTools/skaffold/blob/main/pkg/skaffold/graph/dependencies.go#L91) to this:

```golang
// return getDependenciesFunc(ctx, a, r.cfg, r.artifactResolver)
return []string{}, nil
```
you then can use `useDockerCLI: true` and the build will succeed.

I believe that `skaffold dev` works around this by forcibly rebuilding the cache on filepath/state change [here.](https://github.com/GoogleContainerTools/skaffold/blob/main/pkg/skaffold/runner/listen.go#L92)

Since the hooks are embedded in the skaffold build image function and that happens _after_ tagging, and tagging is where this file dependency cache is built, before hooks cannot currently update/change the already cached docker file dependencies. I'm unsure of the next steps forward to fix this issue.

I'm happy to contribute a PR if y'all could tell me _how_ you want to fix this/general approach.

### Expected behavior
Should be able to have before hooks that move files around and have a docker API build succeed.
With `useDockerCLI` enabled:

### Actual behavior
With `useDockerCLI` disabled (docker API build):

### Information

- Skaffold version: v2.4.0
- Operating system: Ubuntu 24, macOS, ubiquitous.
- Installed via: skaffold.dev, and compiled from source (main/master).
- Contents of skaffold.yaml:

https://github.com/SophisticaSean/skaffold-docker-hook-bug/blob/main/skaffold.yaml
```yaml
apiVersion: skaffold/v4beta1
kind: Config
metadata:
name: skaffold-bug
build:
artifacts:
- image: example
context: example
hooks:
before:
- command: ["bash", "-c", "./example/skaffold_before_hook.sh"]
local:
concurrency: 0
tryImportMissing: false # THIS HAS TO BE FALSE OR CACHE BUSTING WONT WORK
useDockerCLI: false # THIS HAS TO BE TRUE OR THE BEFORE SCRIPT WONT WORK
```

### Steps to reproduce the behavior

1. git clone https://github.com/SophisticaSean/skaffold-docker-hook-bug
2. change `useDockerCLI` in skaffold.yaml to false/true
3. `/bin/rm -rf ./example/cool-files-copy/needed-file.txt; skaffold build --cache-artifacts=true -b example`
4. observe with `useDockerCLI` true, it works, with false it fails saying the file `needed-file.txt` doesn't exist in the docker container.

Logs are not relevant, they don't show anything out of the ordinary as caching doesn't get logged out.