If you're not using static binaries anywhere in the process (a big if) a CheckInstall/installwatch-style solution might work. Basically it uses a library preload to catch all file accesses and redirect them to a temporary area while overlaying the results over the actual filesystem. Then it bundles up all the changes it saw into a package. This is a nice but sub-optimal solution for software lacking true packages, though I use it heavily to make random source-compiled software trackable and uninstallable. However it should work nicely for transactions - just delay committing the overlay until the process completes properly.
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