Use of shell commands when alternatives are available

Maybe supporting windows users isn't a priority (I have no need for it, despite submitting this), but there are a number of places where shell commands could/should be refactored into more portable shutil type commands.

E.g. [cmd_tool_init @ L208](https://github.com/galaxyproject/planemo/blob/ec6e30f8f7106bb749d13d8796145507e6c3d87d/planemo/commands/cmd_tool_init.py#L208), mkdir/cp/mv commands could be replaced.