Dependency confusion attacks exploit a structural gap in software distribution: once a package is installed, there is no cryptographic proof of which registry distributed it. Every existing defense is configuration-based and fails silently when misconfigured. We present a cryptographic distribution provenance system comprising three components: (1) cryptographic registry identity, where every registry holds an Ed25519 keypair and signs every artifact it distributes; (2) a dual-signature model, where the publisher signs at packaging time and the registry countersigns at publication time; and (3) authoritative namespace binding, where consumers pin registry fingerprints and the resolver cryptographically rejects artifacts from unauthorized registries. These create three defense layers requiring simultaneous compromise for a successful attack. A comparison across eight ecosystems (npm, Cargo, Hex.pm, PyPI, Go modules, Docker/OCI, NuGet, Maven) shows no existing ecosystem combines mandatory publisher signing, cryptographic registry identity, mandatory registry countersigning, and consumer-side cryptographic enforcement. The system extends to AI-generation provenance as a signed attribute and governance-enforced dependency resolution. A case study integrates distribution provenance with a three-layer runtime governance architecture, creating a four-phase lifecycle chain with no cryptographic gaps.

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