The Onto Tracker plugin allows users to manage projects within Obsidian based on a defined ontology. It tracks files in a specified folder, categorizes them according to user-defined rules, and maps metadata to align with the ontology. Key features include unpacking ontologies for better understanding, creating 'freezes' to snapshot file states, and applying mappings to update metadata automatically. This functionality supports workflows such as archival and content management by structuring files for further tasks like CMS uploads. Users can define rules based on file types and hierarchies, ensuring flexibility and detailed organization within the vault.