It appears that due to the addition of the puppetfile language to the extension, the puppet resource and the puppet node graph commands no longer appear in the command palate.
This seems to be due to the following lines:
https://github.com/lingua-pupuli/puppet-vscode/blob/15aa7718534edecad5b8e5b34edba048c339c562/package.json#L190
We apparently need to be using editorLangId: microsoft/vscode#26873