fix: treat empty repository directory as uninitialized

[jexjws]

This PR is motivated by ongoing work on the IPFS Desktop Flatpak package for #3042. To reuse the host Kubo repository without granting full home directory access, the Flatpak manifest utilizes --filesystem=~/.ipfs:create. This causes Flatpak to automatically pre-create an empty ~/.ipfs directory on a fresh machine prior to app launch, directly triggering this false-positive "configuration is missing" alert.

When an empty repository directory already exists (such as when pre-created by Flatpak '--filesystem=~/.ipfs:create', user mkdir, or mount points), checkRepositoryAndConfiguration would falsely treat it as a damaged repo missing its config and prompt a warning dialog before initializing it.

Skip verification if the directory is empty or only contains common OS metadata files, allowing ipfsd.init() to proceed as a clean install.

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