Inline notes and collected commentaries are important forms of scholarly communication that evolved within the Confucian exegetical tradition, yet have received little computational attention. Drawing on traditional Chinese exegetics and philology, this paper formulates collected commentary compilation as an NLP task and proposes a computational framework that preserves the contextual dependency of inline notes while enabling their automatic compilation and exegetical knowledge organization. It combines two-step prompt chaining for identifying the associated main-text segments and exegetical functions of annotations with cross-source mention clustering for integrating commentary across editions, achieving a CoNLL F1 score above 97% in a case study on the Classic of Mountains. Our framework lays the foundation for the large-scale organization of historical exegetical knowledge, thereby supporting a broad range of downstream philological and NLP tasks.

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