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I have a project where I need to maintain changes to both the text and binary files. I have a couple of options:

  1. Use patches
  2. Use a versioning system like git or hg.

For my purposes, patches are a better option if it was only text files. However, since there are images that might be replaced/added/deleted, which is the best way to go?

Is there a clean diff/patch utility that can take care of binary differences as well (without me having to specify it is binary -- I should be able to diff the entire directory and not individual files, which I can't with bash's diff in binary mode) and use them as patches? If not, which versioning system is a cleaner option when it comes to binary files?

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Mercurial has the notion of patch queue (with the mq extension enabled), largely inspired by quilt.
This allows you to manage your patches in several ways:

  • Use a single patch queue and have all your patch order sequentially in it
  • Use several patch queues, with the qqueue command, and have patches grouped by whatever criteria fits you.

As a bonus, as patches queues are really patch files, you can easily change their order and even move/copy them from one queue to another (have a look in your .hg directory to find the patch queues).

You can find a lot more of usefull information about managing patch queues at Steve Losh's tutorial on mercurial queue.

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Both Git and Mercurial can easily handle both text and binary files. Use whichever you prefer. And yes, a VCS is the right choice.

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VCS makes managing this a lot more complicated, believe it or not. For my purposes, its a lot cleaner if everything can be done in terms of some kind of patches and the patches are maintained in a repository.
A VCS is nothing else than a tool around such a repository containing patches.
@Vanwaril: It sounds like what you might be looking for is a patch queue? If so, there are projects that implement patch queues on top of both Mercurial and Git. For Mercurial, see hg mq, for Git, see git.wiki.kernel.org/index.php/…
Mercurial and Git can make binary patches.
@Vanwaril: hg mq can handle different patch queues (have a look at stevelosh.com/blog/2010/08/… ). More over you can easily change the patch order as long as they are really independent.
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If you don't like a VCS as such, try using a ftp server containing patches. Version numbers can be used as directory names. This system can be backed with a script, which applies patches sequentially based on directory names.

In the project I'm working on, database patches are applied in this manner. However, they are maintained inside a VCS. A file can be used to maintain the current version, which will be read by the script to decide which patch to apply.

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