I would like to use the advance Angular JSS project as an starting point for a code first approach but I would like to know if it is possible to remove all components that came with that Angular project from the code itself?. Removing the components from the manifest and the data folder didn't affect the the Sitecore tree or templates at all.
For your own safety, by default the JSS import will not delete any items. You can enable
Full Wipe Mode if you wish for the app's items to be cleared prior to import. You can do this, or just manually remove the items. If they're not in the manifest definitions, they won't come back.
For more info, see JSS docs on full wipe mode.