This paper introduces Primary Breadth-First Development (PBFD) and Primary Depth-First Development (PDFD)—formally and empirically verified methodologies for scalable, industrial-grade full-stack software engineering. Both approaches enforce structural and behavioral correctness through graph-theoretic modeling, bridging formal methods and real-world practice.PBFD and PDFD model software development as layered directed graphs with unified state machines, verified using Communicating Sequential Processes (CSP) and Linear Temporal Logic (LTL). This guarantees bounded-refinement termination, deadlock freedom, and structural completeness.To manage hierarchical data at scale, we present the Three-Level Encapsulation (TLE)—a novel bitmask-based encoding scheme. TLE operations are verified via CSP failures-divergences refinement, ensuring constant-time updates and compact storage that underpin PBFD's robust performance.PBFD demonstrates exceptional industrial viability through eight years of enterprise deployment with zero critical failures, achieving approximately 20× faster development than Salesforce OmniScript, 7–8× faster query performance, and 11.7× storage reduction compared to conventional relational models. These results are established through longitudinal observational studies, quasi-experimental runtime comparisons, and controlled schema-level experiments.Open-source Minimum Viable Product implementations validate key behavioral properties, including bounded refinement and constant-time bitmask operations, under reproducible conditions. All implementations, formal specifications, and non-proprietary datasets are publicly available.