Improve usage with spaces in folder names on Windows/Mac/Linux [fixed]

Adding on to #256, there are many usage of `os.system()` in the package codebase, especially to automates setup process.

But the way of calling `os.system()` doesn't have double quotes around the folder and filename. This would lead to error on folders with spaces. Creating this issue to improve the package ease-of-use for user environments with spaces in folders.