Obviously the indictment wasn’t written to be technical and/or by someone who understands technology.
For instance:
The portion of the password Manning gave to Assange to crack was stored as a ‘hash value’ in a computer file that was accessible only by users with administrative-level privileges
… Okay, a “hash value” is something that cannot be reversed (you can find a set of possible sources for the hash, “collisions”, but it is “one way” only). If the file storing these hashes was only available to administrative users, then how did Manning get it? If instead the indictment is saying that administrative users viewed the file as unencrypted somehow: that’s not how hashes work (these would instead be “encrypted” using ex AES).
From this, the best I can tell is that Manning pulled the /etc/passwd file, which contains hashed versions of users’ passwords, from which she (and Assange) hoped to glean an administrative password with which they could then get access to more files on the system. Note that at some point the /etc/passwd file (readable by anyone who can access the machine) moved to /etc/shadow (readable only by “root” superusers, who would of course already have access to the rest of the contents of the machine already), so I’m assuming this was running an older version of Linux with /etc/passwd. Also note that if Manning/Assange had any real hope of finding a hash collision there, they either thought the admin used a simple password, or they knew that the system was using an old and crackable hashing scheme (say, MD5 or DES rather than bcrypt or newer).
I’m also assuming that the “special software” Assange used was a script-kiddie level (or maybe more sophisticated; Assange isn’t exactly a dummy although he does do a good job of playing one on TV) brute force hash cracking tool running on Linux, rather than somehow Linux itself.
I did also laugh at the apparent assertion that Linux is that “special software”, then had the gut-wrenching realization that somewhere someone’s crazy uncle has already internalized the “fact” that “Linux” is one of them “hacker tools” that means its users must be up to no good.