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Quote variables where possible in scripts

Fredrik Wieczerkowski requested to merge quote-variables into master

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).

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