push: make sure source files exist before applying changes

[efiop]

In cloud versioning case when we delete our cache and workspace data and try to dvc push, it will think that it needs to modify/relink a file and in order to do that will delete it but then fail to create a new one because it will turn out that there is no source for data.

We need to add a step that will filter out missing data (probably somewhere even before index.checkout.compare()) from a desired index, so that we don't even think that we can create those missing files.

One of our users already ran into this.

This also applies to dvc checkout and possibly other operations (don't think so, but need to check).

[efiop]

Fixed by iterative/dvc-data#482 in #10181

Regarding checkout, it is mitigated by the fact that we double check files that we might delete, though that behaviour is a bit contraversial as well and might be changed in the future (to not delete unless we have a file to replace it with, even if deleted file is also in the cache).

There is one more unrelated issue about pulling missing files, but I'll introduce a fix separately. (EDIT: see #10188)