This makes merging somewhat harder in complex cases. The merge view (see screenshot) has only 3 panes, just like SourceGear Diff/Merge. So you can have some history diff on all files much simpler. Meld is a newer free tool that I'd prefer to SourceGear Diff/Merge: Now it's also working on most platforms (Windows/Linux/Mac) with the distinct advantage of natively supporting some source control like Git.
Check that merge screens-shot and you'll see it's has the 3 views at least. SourceGear Diff/Merge may be my second free tool choice. Perforce tries to make it a bit hard to get their tool without their client.
You cannot edit manually the files and you cannot manually align. My main disappointement with that tool is its kind of "read-only" interface. The Perforce Visual Client ( P4V) is a free tool that provides one of the most explicit interface for merging (see some screenshots). It has many features like advanced rules, editions, manual alignment. It integrates with many source control and works on Windows/Linux. It's somewhat less visual than P4V but way more than WinDiff. The good thing with its merge is that it let you see all 4 views: base, left, right, and merged result. Beyond Compare 3, my favorite, has a merge functionality in the Pro edition.
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