Currently we manage a list of in-progress compactions in a system table, which we use to cleanup incomplete compactions when we're done. The problem with this is that 1) it's a bit clunky (and leaves us in positions where we can unnecessarily cleanup completed files, or conversely not cleanup files that have been superceded); and 2) it's only used for a regular compaction - no other compaction types are guarded in the same way, so can result in duplication if we fail before deleting the replacements.
I'd like to see each sstable store in its metadata its direct ancestors, and on startup we simply delete any sstables that occur in the union of all ancestor sets. This way as soon as we finish writing we're capable of cleaning up any leftovers, so we never get duplication. It's also much easier to reason about.