Including Tools in the Repo
As an alternative to binary patches to make arbitrary changes, we could simply include the tools to make such changes within the repo itself, and a wrapper to make it easy to run them.
A reasonable way to do this would be to create a binary directory alongside the installed mods where tools such as tes3cmd, tr-patcher, fix_nif, etc. get installed and then have a wrapper to execute files within that directory that other mods can use.
To handle the dependencies of these tools, we could use something akin to system dependencies to ensure that the user can't install them without a usable perl/java installation, or without pyffi installed.
I.e. we have a system category containing packages such as, for example, system/perl, which will fail to install if a usable perl installation is not found, prompting the user to install perl. A tool such as tes3cmd would depend on this package. (Unfortunately, the idea of calling everything in the repo a mod breaks down at this point).