[BUGFIX] Add back --prefix when installing dependencies

[ricardo-devis-agullo]

Apparently, for some reason still unknown to me, when calling publish inside a build agent, doing a npm install without the prefix may not create a node_modules folder (could not reproduce in local, but I could on Azure Devops), when you call npx oc publish on a folder that does not have a package.json.

For this reason I'm adding the option to choose whether to add the --prefix or not. It will be added when installing missing dependencies (used by publish and dev), but not when installing the template or the compiler (so it still works correctly without nesting node_modules), because installing the template will always do npm init first