documentation: use paths relative to toplevel dir
This change is done to reduce ambiguity in some cases;
the previous intention has been to ease navigation when
staying in a particular directory, now it's been changed
in favour of convenient toplevel `git grep' in fact.
Both variants have their pros and cons, I just find myself
leaning to this one by now hence the commit. Feel free to
provide constructive criticism :)
Some path-related bitrot has also been fixed while at that.
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