The open-source ecosystem on GitHub lacks a systematic hierarchical taxonomy of software repositories. GitHub Topics, the dominant organizational mechanism, is flat, inconsistent, and covers only 67% of projects. We present ATLAS, the first framework that automatically constructs a hierarchical taxonomy for software repositories and classifies projects into it end-to-end. By combining LLM global knowledge with real repository distributions, ATLAS proposes meaningful splitting dimensions and iteratively corrects those that fail to accommodate real projects. A Designer Agent proposes splitting dimensions while a Classifier Agent assigns repositories; a self-corrective refinement loop uses classification failures to drive dimension revision through escalating strategies. We evaluate ATLAS on 54,387 GitHub repositories against six baselines spanning four paradigms, two downstream tasks, and three model families. On a stratified 2,001-repository benchmark, ATLAS achieves a Taxonomy Quality F-score (TQF) of 83.13%, outperforming the best baseline by 15 percentage points (on the full 54k corpus the approximate TQF is 73.0%, a gap driven by Path Granularity's all-or-nothing scoring on longer paths rather than lower classification accuracy). It is the only method to simultaneously achieve high structural quality and high practical applicability. On downstream tasks, ATLAS enables alternative discovery with P@1 = 85.71%, surpassing even human-curated lists (62.34%), and achieves the highest P@1 for repository retrieval. The taxonomy further reveals structural ecosystem trends that are difficult to obtain from flat tags or similarity methods: the shift from libraries to AI/ML applications (now 61% of newly community-adopted projects) becomes visible only through hierarchical, type-based categorization. An interactive taxonomy explorer is available at https://atlas-taxonomy.netlify.app/

翻译：暂无翻译