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As of pnpm v3, pnpm fails if the configs that were used when creating node_modules differ from the present ones. For instance, if independent-leaves is set to false globally but installation was done using pnpm install --independent-leaves. Running pnpm add foo will fail. Only pnpm add foo --independent-leaves will work These changes are making this less strict. If node_modues was created using some configs, installation will only fail if the present configs are set locally (or via CLI flags) and they have incompatible values. So if pnpm install --independent-leaves was used, then pnpm add foo will work. But pnpm add foo --no-independent-leaves will fail. PR #2034