One Repository, Multiple Instruction Files: Semantic Divergence in One Hash-Selected Pair Across the First 150 Eligible Repositories

Repositories can contain several persistent instruction files under different path conventions. Their relationships have not been measured with a denominator that first separates reference adapters from separate non-delegating, closure-expanded analysis bodies. This preregistered cross-sectional content analysis used version 4 of a public coding-agent configuration dataset. The first 200 of 455 ordered non-pilot candidates were reference-screened; the first 150 eligible repositories supplied one hash-selected pair each. Pair selection was semantic-outcome-independent conditional on content-derived reference eligibility. Separately tasked GPT-5/Codex agents classified explicit propositions across five dimensions; a random 38-pair subset was blindly recoded within the same AI-agent environment, and no independent human recoding was performed. Actionable semantic divergence occurred in 19/150 selected pairs (12.7%, Wilson 95% CI 8.3%–18.9%), direct contradiction in 6/150 (4.0%, 1.8%–8.5%), and the analytically separate unilateral mandatory-workflow asymmetry in 35/150 (23.3%, 17.3%–30.7%). A post hoc 1,000-seed selection diagnostic produced 17–20 positives per 150 pairs. The all-pairs sensitivity within the same repositories produced 23/199 actionable pairs (11.6%, repository-cluster bootstrap 95% CI 6.8%–16.8%). Most selected pairs were Complementary. The study contributes three linked outputs: a reference-aware measurement design, a bounded selected-pair baseline, and an auditable derived-evidence package. It does not establish temporal drift, human intercoder reliability, or downstream effects on agents or software. Preregistration: https://doi.org/10.17605/OSF.IO/3U2B9 The English manuscript is the authoritative version. Article text, schemas, and derived annotations are licensed CC BY 4.0; original code is MIT-licensed; third-party materials retain their original licenses. Raw and extracted third-party repository files are not redistributed. Correction and takedown contact: batteryofsprunk@gmail.com