feat(federation): activate verified corpus graphs

[tcballard]

Stack

1. docs(federation): ratify graph-complete v0.29 scope #462 — ratify graph decisions
2. feat(federation): establish graph engine foundation #463 — graph foundation
3. This PR — activate the verified graph engine
4. feat(federation): certify graph profile and evaluation #465 — profile guidance and DecisionGrounding evidence

What this implements

• manifest v2 with multiple direct parents and bounded recursive DAG composition
• independently verified physical routes, cycle/divergent-pin detection, and diamond deduplication
• global corpus.source::canonical-id resolution with source-contextual aliases
• equal cross-source IDs as deterministic ambiguity rather than precedence
• explicit Decision-backed override chains and diamond convergence
• one catalog/effective/root-local model across validation, resolution, retrieval, routing, gate, Sentry, exports, MCP, and audit
• closure generation v3 and isolated store/v3 persistence with fail-closed freshness and corruption repair
• complete source/layer/pin, override-chain, and topology-route provenance
• read-only enforcement across every direct, transitive, and duplicate materialisation route
• additive viewer/documents/graph exports and source-aware Portal navigation
• exact v1 and no-manifest compatibility paths

Hardening

The implementation uses stable captured bytes throughout digesting, parsing, validation, composition, persistence, and serving. It rejects unsafe YAML, symlink/reparse traversal, hard-linked inherited files, mount boundaries, path escapes, stale pins, invalid topology, and unsafe output/cache targets.

Validation

• cargo test --workspace --all-targets --locked --no-fail-fast — passed
• cargo clippy --workspace --all-targets --locked -- -D warnings — passed
• graph CLI contract — 9/9
• graph MCP contract — 5/5
• v1 federation CLI — 14/14
• v1 federation MCP — 8/8
• decided validate decisions/ — 468 valid, 0 invalid, 12 skipped
• decided relationships decisions/ --validate — 3,055 checked, 0 issues
• decided gate decisions/ --json — 0 blocking, 134 existing advisories
• decided review decisions/ --json — 508 non-blocking issues, health 96
• agent-rules drift check — in sync
• Linux, Windows, and macOS cross-platform certification — passed

Review and merge after #462 and #463.

Closes #270
Closes #272

[tcballard]

Cross-platform certification — passed

The complete native matrix passed for this PR head.

• Linux: native release build; export-schema contracts; inotify/stat freshness; workspace unit and bounded regression suites; strict all-target Clippy; authoritative spec registry and byte-vector guards; MCP compatibility vectors; live-corpus invariants
• Windows: native release build; CLI and cache/store runtime smoke; MCP contract smoke
• macOS: native release build; CLI and cache/store runtime smoke; MCP contract smoke
• Dependency policy: cargo-deny passed
• PR checks: passed

Workflow evidence: rust-spike run #207 (run ID 31387274390); PR Checks run #530.