How do I "diff" multiple files against a single base file?

None of the existing diff/merge tools will do what you want. Based on your sample screenshot you're looking for an algorithm that performs alignments over multiple files and gives appropriate weights based on line similarity.

The first issue is weighting the alignment based on line similarity. Most popular alignment algorithms, including the one used by GNU diff, TDiff, and TrmDiff, do an alignment based on line hashes, and just check whether the lines match exactly or not. You can pre-process the lines to remove whitespace or change everything to lower-case, but that's it. Add, remove, or change a letter and the alignment things the entire line is different. Any alignment of different lines at that point is purely accidental.

Beyond Compare does take line similarity into account, but it really only works for 2-way comparisons. Compare It! also has some sort of similarity algorithm, but it also limited to 2-way comparisons. It can slow down the comparison dramatically, and I'm not aware of any other component or program, commercial or open source, that even tries.

The other issue is that you also want a multi-file comparison. That means either running the 2-way diff algorithm a bunch of times and stitching the results together or finding an algorithm that does multiple alignments at once.

Stitching will be difficult: your sample shows that the original file can have missing lines, so you'd need to compare every file to every other file to get the a bunch of alignments, and then you'd need to work out the best way to match those alignments up. A naive stitching algorithm is pretty easy to do, but it will get messed up by trivial matches (blank lines for example).

There are research papers that cover aligning multiple sequences at once, but they're usually focused on DNA comparisons, you'd definitely have to code it up yourself. Wikipedia covers a lot of the basics, then you'd probably need to switch to Google Scholar.

• Sequence alignment
• Multiple sequence alignment
• Gap penalty

For people that are still wondering how to do this, diffuse is the closest answer, it does N-way merge by way of displaying all files and doing three way merge among neighboors.