RF: Prompt user if they would like to remove archive directory

The fsl_add_module command now asks the user if they would like to remove the archive directory - this may be useful for people with limited disk space. This can be done automatically with the new --remove command-line flag.

This MR also fixes an issue where the presence of a file or directory with the same name as an official manifest (e.g. ~/fslcourse) would cause fsl_add_module to try to load it as the manifest.