Add graph-storage crate

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Code Review

This pull request introduces the graph-storage crate, which provides a delta-based graph representation for the Graphite file format, including CRDT/delta computation, conversion utilities, and round-trip tests. It also cleans up legacy migrations in graph-craft and updates MemoHash to compare values instead of hashes. The review feedback highlights a potential DoS/OOM vulnerability when resizing the exports vector with unvalidated slot indices, suggests optimizing the O(N^2) pairwise comparison in order_consistent to O(N log N) by sorting, and recommends using into_iter().next() instead of drain(..).next() for idiomatic element extraction.

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[cubic-dev-ai]

9 issues found across 26 files

Confidence score: 2/5

• There are multiple high-confidence, user-impacting regressions (sev 7–8) across hashing, graph diffing, and serialization, so merge risk is currently high rather than routine.
• Most severe: node-graph/libraries/core-types/src/memo.rs makes MemoHash equality ignore hash while Hash still includes it, which can violate hash collection invariants and cause incorrect map/set behavior.
• Several storage/runtime paths risk dropped or corrupted data: missed network/export diffs in document/graph-storage/src/delta.rs, omitted export-only resources in document/graph-storage/src/from_runtime.rs, and silent truncation in document/graph-storage/src/to_runtime.rs when inputs lengths differ.
• Pay close attention to node-graph/libraries/core-types/src/memo.rs, document/graph-storage/src/delta.rs, document/graph-storage/src/from_runtime.rs, document/graph-storage/src/to_runtime.rs, and node-graph/libraries/resources/src/lib.rs - they contain the highest-likelihood correctness and round-trip integrity risks.

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[cubic-dev-ai]

11 issues found across 19 files

Confidence score: 2/5

• Multiple high-severity, high-confidence data-integrity risks make this PR risky to merge as-is, especially in core graph storage/CRDT paths (document/graph-storage/src/attributes.rs, document/graph-storage/src/to_runtime.rs, document/graph-storage/src/crdt.rs, document/graph-storage/src/ids.rs).
• The most severe issue is inconsistent Priority equality/ordering/hashing in document/graph-storage/src/attributes.rs, which can break HashMap/BTree* behavior and lead to hard-to-debug corruption-like behavior.
• There are additional concrete regression risks affecting user-visible state correctness: duplicate node IDs can silently collapse nodes during runtime reconstruction, deletes can be resurrected without tombstones, and non-canonical Rev hashing can make identical deltas produce different IDs.
• Pay close attention to document/graph-storage/src/attributes.rs, document/graph-storage/src/to_runtime.rs, document/graph-storage/src/crdt.rs, document/graph-storage/src/ids.rs, document/graph-storage/src/session.rs, document/graph-storage/src/delta.rs, document/graph-storage/src/model.rs - core invariants and history/diff behavior can diverge from expected graph state.

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[cubic-dev-ai]

3 issues found across 19 files

Confidence score: 3/5

• There is meaningful regression risk in document/graph-storage/src/session.rs: the unconditional registry reset can drop visible hot-zone edits and desynchronize working state from hot_log when unretired ops are present, which is user-facing state integrity impact.
• document/graph-storage/src/session.rs also has a fallible path in commit_ops that currently uses assert! for missing parents, so malformed or unexpected input could panic the app instead of returning an error.
• document/graph-storage/src/ids.rs deriving Default for LamportClock introduces an ambiguous/invalid construction path without an explicit PeerId; this is moderate API correctness risk rather than an immediate blocker.
• Pay close attention to document/graph-storage/src/session.rs, document/graph-storage/src/ids.rs - state rebuild correctness, panic-free error handling, and explicit clock initialization need validation before merge.

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[cubic-dev-ai]

5 issues found across 19 files

Confidence score: 2/5

• There are concrete regression risks in core behavior: document/graph-storage/src/document.rs can drop the root delta in history iteration, which can break history-based restoration when a removal happens at the root commit.
• document/graph-storage/src/to_runtime.rs lacks same-network validation during node-reference remapping, so cross-network references may be converted into wrong or dangling runtime IDs instead of failing fast.
• Additional medium-severity correctness issues in document/graph-storage/src/attributes.rs (finite-value invariant bypass for Priority) and document/graph-storage/src/delta.rs (nondeterministic diffs from HashSet iteration) increase the chance of inconsistent state and revision behavior.
• Pay close attention to document/graph-storage/src/document.rs, document/graph-storage/src/to_runtime.rs, document/graph-storage/src/attributes.rs, and document/graph-storage/src/delta.rs - they contain the highest-impact correctness and determinism risks before merge.

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[cubic-dev-ai]

5 issues found across 19 files

Confidence score: 2/5

• There are concrete correctness risks in core data behavior, so this looks higher risk than a typical merge despite being fixable.
• In document/graph-storage/src/resources.rs, the sources sorted-order invariant is assumed by binary-search-based operations but not enforced, which can silently corrupt source-chain behavior for unsorted external/deserialized data.
• In document/graph-storage/src/crdt.rs and document/graph-storage/src/delta.rs, timestamp tombstones for attribute deletes are dropped (allowing stale resurrection under out-of-order delivery) and inputs_attributes length changes are missed in structural diffing, both of which can cause convergence or delta-loss regressions.
• Pay close attention to document/graph-storage/src/resources.rs, document/graph-storage/src/crdt.rs, and document/graph-storage/src/delta.rs - they contain the user-impacting correctness paths (ordering invariants, LWW tombstones, and diff completeness).

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[cubic-dev-ai]

6 issues found across 19 files

Confidence score: 2/5

• Current risk is high because Delta.id in document/graph-storage/src/crdt.rs is trusted during deserialization without validating against the content hash, which can undermine revision integrity via crafted history-key spoofing/collision.
• document/graph-storage/src/resources.rs and node-graph/libraries/resources/src/lib.rs both introduce concrete data-correctness risk: duplicate on-disk keys can break binary-search behavior, and 64-bit ResourceId truncation can collide distinct resources and merge mappings incorrectly.
• There are also stability concerns in document/graph-storage/src/ids.rs where compute_rev and mint_node_id use expect, so recoverable failures may become process crashes; this is important but likely straightforward to harden.
• Pay close attention to document/graph-storage/src/crdt.rs, document/graph-storage/src/resources.rs, node-graph/libraries/resources/src/lib.rs, and document/graph-storage/src/ids.rs - integrity validation, key invariants, ID collision handling, and panic paths are the main merge blockers.

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[cubic-dev-ai]

5 issues found across 19 files

Confidence score: 3/5

• There is a concrete regression risk in document/graph-storage/src/from_runtime.rs: dropping scope_injections during runtime→storage conversion can silently lose graph behavior on round trips, which is user-impacting and raises merge risk.
• document/graph-storage/src/resources.rs has correctness and stability concerns (has_embedded_source using raw JSON equality and panicking expect(...) in ResourceEntry::embedded), which could lead to duplicate embedded fallbacks or editor crashes instead of handled errors.
• document/graph-storage/src/crdt.rs and document/graph-storage/src/crdt_tests.rs show undo/test reliability gaps (is_gesture_end treating any marker as true, and a test not asserting is_err()), so behavior around gesture boundaries and error-path coverage is less certain.
• Pay close attention to document/graph-storage/src/from_runtime.rs, document/graph-storage/src/resources.rs, document/graph-storage/src/crdt.rs, and document/graph-storage/src/crdt_tests.rs - data-loss-on-conversion, embedded-source detection, panic handling, and gesture/error-path correctness need validation before merge.

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