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WinMerge's auto-merge assumes the following order of files, depending on which pane is currently active(It’s a little inconsistent...):

  • Middle pane: assumes that the files are in the order [theirs]-[base]-[mine], and merges the unconflicted changes in left (theirs) and right (mine) into middle (base).
  • Right pane: assumes that the files are in the order [base]-[theirs]-[mine], and merges the non-conflicting changes in middle(theirs) into right(mine).
  • Left pane: assumes that the files are in the order [mine]-[theirs]-[base], and merges non-conflicting changes in the middle (theirs) into the left (mine).

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@schierlm
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