You can't fix this because the format in the repostiory is the old metadata format which is not supported in VS Code.
Because legacy tools such as Force.com IDE used the metadata format,
you can’t directly open your such projects in VS Code. You must either
convert your metadata to source format (using sfdx
force:mdapi:convert) or create a new project and then retrieve the
metadata from your org using the manifest (package.xml file) that you
used in your previous IDE.
The question you should ask them is why they don't update their repository to the source format which IntelliJ/Illuminated Cloud also supports. This would allow the developers to choose their tool as well as be better suited for source control development as highlighted by the documentation. If you're using source control, your repository should be in the source format.
The commands that Salesforce Extensions for VS Code uses to push,
pull, deploy, and retrieve your source assume that your files are in
source format (rather than metadata format). Source format is
optimized for working with version control systems.
You can utilize the CLI to convert projects pretty easily with:
And then pushing all the changes to your repository.