refactor(proto): isolate gateway storage messages

[varshaprasad96]

Summary

Separates persistence-only protobuf messages from OpenShell's public API packages. The gateway now owns a private, versioned storage package while preserving existing payload bytes and stable database object routing.

Related Issue

Closes #3053

Changes

• Move seven storage-only messages into the server-private openshell.storage.v1 package and compile them only for the gateway.
• Remove storage-only symbols from public descriptors and regenerated Go SDK bindings; Python and TypeScript generation remain public-only.
• Add descriptor-derived gates for all 77 public RPCs, 13 durable roots, their transitive schemas, and their exact overlap.
• Add v0.0.116 payload fixtures that survive an on-disk SQLite reopen, current migrations, and current persistence loaders byte-for-byte.
• Document every dual-purpose persisted root and the separate public-wire/storage-migration compatibility policies.

Deviations from Plan

None — implemented as planned.

Testing

• mise run pre-commit passes
• mise run test passes
• mise run ci passes
• Unit tests added/updated
• E2E tests added/updated (not applicable; no runtime, sandbox, policy, or infrastructure path changed)

Tests added:

• Unit: private storage schema freeze, public SDK/descriptor exclusion, public/durable closure inventories, and v0.0.116 semantic decode coverage.
• Integration: on-disk SQLite fixture reopen through current migrations and persistence loaders with exact payload preservation.
• E2E: N/A; no files under e2e/ changed.

Checklist

• Follows Conventional Commits
• Commits are signed off (DCO)
• Architecture docs updated

Documentation updated:

• architecture/gateway.md records storage classifications, per-root twin decisions, schema inventories, and compatibility policy.

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[politerealism]

Reviewed the full diff (excluding the generated Go SDK bindings, which mechanically follow the .proto changes).

Summary: Moves seven server-internal, storage-only protobuf messages out of the public openshell.proto into a new private openshell.storage.v1 package compiled only into openshell-server, so they no longer leak into the public API descriptor set or generated SDK bindings.

What stood out positively:

• The core safety claim — that relocating a message's package is compile-time-only and requires no data migration, since protobuf wire bytes don't encode package names — is proven with real byte fixtures, not just asserted. storage_proto.rs decodes checked-in hex payloads produced by the old public-package types using the new private types, and separately round-trips them through an actual on-disk SQLite database via current migrations.
• Schema drift is caught by fingerprint tests (SHA-256 over the storage schema, public RPC closure, durable-root closure, and their overlap), each failing with an actionable message telling the developer exactly what to review before updating the hash.
• The nine types that remain deliberately dual-purpose (Sandbox, Provider, Workspace, etc.) are an explicit, reviewed accept documented in architecture/gateway.md, not an oversight — and that overlap is exactly what the fingerprint test guards going forward.
• storage_types_are_absent_from_public_descriptor is a good explicit negative check, not just an implicit "it compiles" assumption.

No concerns that warrant a change. Solid, well-tested refactor.

LGTM.