Quote variables where possible in scripts

Currently there are few subtle issues where the scripts won't deal with paths containing spaces correctly. This is especially problematic on Windows where paths like C:\Program Files\... are common and e.g. often already contained by the path to the user's Prolog interpreter. This PR attempts to fix this by quoting as may path-ish variables as possible (which is good practice anyway since using unquoted expansions in combination with commands like rm can e.g. lead to unexpected deletions).