The docs state that if you have a visual diff tool installed, like meld, running VC->*->Diff will use that tool. This appears to work for VC->File->Diff, but not for VC->Directory->Diff, which spits out the default diff output.
Thinking that GeanyVC was using `git diff`, I tried overriding the `git diff` with:
git config --global diff.external meld
but this has no effect, since GeanyVC appears to ignore git's `diff.external` setting, preventing the use of a visual diff tool.