An Operating System (OS) combines multiple interdependent software packages, which usually have their own independently developed architectures. When a multitude of independent packages are placed together in an OS, an implicit inter-package architecture is formed. For an evolutionary effort, designers/developers of OS can greatly benefit from fully understanding the system-wide dependency focused on individual files, specifically executable files, and dynamically loadable libraries. We propose a framework, DepEx, aimed at discovering the detailed package relations at the level of individual binary files and their associated evolutionary changes. We demonstrate the utility of DepEx by systematically investigating the evolution of a large-scale Open Source OS, Ubuntu. DepEx enabled us to systematically acquire and analyze the dependencies in different versions of Ubuntu released between 2005 (5.04) to 2023 (23.04). Our analysis revealed various evolutionary trends in package management and their implications based on the analysis of the 84 consecutive versions available for download (these include beta versions). This study has enabled us to assert that DepEx can provide researchers and practitioners with a better understanding of the implicit software dependencies in order to improve the stability, performance, and functionality of their software as well as to reduce the risk of issues arising during maintenance, updating, or migration.