Tool for 3-Way Binary (Hex) File Comparison?

Question

I have a set of binary configuration files with three versions each -- an original, and two differently-modified versions of each file. I need to be able to see the differences

Answer 1

Vim has a built-in diff tool that can compare an arbitrary number of files. It also runs on Windows. You can find it at http://vim.org.

The standard installation of vim for windows includes xxd, which allows you to see binary files as text:

So for example if you try:

xxd xxd.exe

you'll get:

0000000: 4d5a 9000 0300 0000 0400 0000 ffff 0000  MZ..............
0000010: b800 0000 0000 0000 4000 0000 0000 0000  ........@.......
0000020: 0000 0000 0000 0000 0000 0000 0000 0000  ................
0000030: 0000 0000 0000 0000 0000 0000 d800 0000  ................
0000040: 0e1f ba0e 00b4 09cd 21b8 014c cd21 5468  ........!..L.!Th
0000050: 6973 2070 726f 6772 616d 2063 616e 6e6f  is program canno
0000060: 7420 6265 2072 756e 2069 6e20 444f 5320  t be run in DOS 
0000070: 6d6f 6465 2e0d 0d0a 2400 0000 0000 0000  mode....$.......
0000080: 6ba7 bec3 2fc6 d090 2fc6 d090 2fc6 d090  k.../.../.../...

etc...

So you can use xxd to dump your binary files into text files:

xxd orig > orig.txt
xxd mod1 > mod1.txt 
xxd mod2 > mod2.txt

And then run vim in diff mode:

vim -d orig mod1 mod2

And this will give you something like this:

(This screenshot was taken from here and is no more than an illustration of what a 3-way diff will look like in VIM)

All of these tools are available in windows, so they should solve your problem.

Edit:

After you merge the results of xxd, you can convert the hex dump into a binary file using xxd -r:

xxd -r merged_xxd_file merged_binary_file

You can see more details and options in xxd's manpage