So it seems that SquirrelMail 1.4.11 and 1.4.12 were recently backdoored. Similar to some high-profile backdoors in the past, this was done by modifying the distribution tarball on rather than infiltrating the source code repository . In this case, the backdoor was detected when a user noticed that the MD5 published on SquirrelMail's website didn't match the calculated MD5 from the SourceForge distribution.
Since the SVN repository remained intact, we can't go back and examine the backdoor in detail. However, we do have a newsgroup posting that sheds a little light on the situation:
> What diff do you see between the compromised version and
> the one that is there now? I see only a comment diff in one file.
it was a small block of code that checks for a $_SERVER var. If that var was present, it would redefine SM_PATH. Under normal circumstances, this would never be executed, but we have since learned how to make it execute.
In PHP, $_SERVER is an array populated by the web server that contains information such as headers, paths, and script locations. This includes some user-supplied input such as the URL query string and the HTTP headers. SM_PATH is the filesystem path where SquirrelMail is configured to be run from. So once an attacker controls SM_PATH, it's likely that a subsequent call to include() can be exploited to fetch and execute PHP code from a remote server. This is a typical example of a Remote File Include vulnerability.
Note that the attacker backdoored the 1.5.1 distribution as well, with the same type of vulnerability but at a different location in the codebase.
I think what's most interesting to me about this is that so many open source projects still rely on MD5 hashes for integrity checking. The minute the Xiaoyun Wang paper on MD5 collisions was released, every security practitioner in the world considered MD5 unsafe from that point forward. Even though practical attacks had not yet been formulated, the writing was on the wall. Unfortunately, the rest of the world either didn't notice or didn't care.
Cryptographers have since developed increasingly sophisticated attacks stemming from Wang's original work. Recently, researchers in the Netherlands demonstrated two examples of chosen-prefix attacks which would make it possible for an attacker to take two tarballs (one original, one backdoored) and append a series of bytes to each that result in both files having the same MD5 hash. This proves beyond a shadow of a doubt that MD5 is not an effective method for verifying software integrity. There was hardly any doubt that this attack would surface eventually, so why is MD5 still in such widespread usage?
Cryptographic weaknesses aside, a lot of people completely miss the mark with hashes. MD5 or SHA-1 (or any hash function) are not very effective if the only way a user can verify them is on the same website where the download is hosted. If the download point is compromised, chances are the attacker can modify the hashes printed on the website too. Even when it's done correctly, hashes only help identify when the distribution point is compromised. It does nothing to protect against source code compromise or vulnerabilities in the development tool chain.
 Static Detection of Backdoors, Chris Wysopal and Chris Eng, 2007.