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Hm, are you sure it is indeed because you're painting water tiles blue? I've mapped out 4F and 5F, as well as three-fifths of the next stratum (at least two of those floors have a fishing pond) in the "incorrect" way you described and I still get credit. I also do similar with 2nd-stratum "pit" tiles (I mark them grey), again with no issue.
War Magi in EO 2 U don't actually have any inherent Sword skills, only War Edge skills that have War Edge Mastery as a prerequisite anyway. Combined with the phrasing of the skill description, this "bug" would appear to actually be "working as intended."
War Magus does have inherent sword skills. War Edge skills are simply just sword skills with a special name. Anyone with a sword can use them regardless of circumstance.
War Edge Mastery simply lets the user use sword skills with a staff.
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How well does it match the trope?