To prevent making unnecessary heavy calls to the backend, we should use a search query to limit the result.
But even if we use a search query, we should still use the pagination details to make sure we retrieved all items.
In TFE you can configure a workspace to use a custom working directory. When determining which directory that needs to be uploaded to TFE, this working directory should be taken into account to make sure we are uploading the correct root directory for the workspace.
Sander van Harmelen