A large user base relies on software updates provided through package managers. This provides a unique lever for improving the security of the software update process. We propose a transparency system for software updates and implement it for a widely deployed Linux package manager, namely APT. Our system is capable of detecting targeted backdoors without producing overhead for maintainers. In addition, in our system, the availability of source code is ensured, the binding between source and binary code is verified using reproducible builds, and the maintainer responsible for distributing a specific package can be identified. We describe a novel "hidden version" attack against current software transparency systems and propose as well as integrate a suitable defense. To address equivocation attacks by the transparency log server, we introduce tree root cross logging, where the log's Merkle tree root is submitted into a separately operated log server. This significantly relaxes the inter-operator cooperation requirements compared to other systems. Our implementation is evaluated by replaying over 3000 updates of the Debian operating system over the course of two years, demonstrating its viability and identifying numerous irregularities.