Add graph-storage crate

[TrueDoctor]

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[gemini-code-assist]

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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[TrueDoctor]

@cubic-ai-dev

[cubic-dev-ai]

@cubic-ai-dev

@TrueDoctor I have started the AI code review. It will take a few minutes to complete.

[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.

<sub>Reply with feedback, questions, or to request a fix.

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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.

<sub>Reply with feedback, questions, or to request a fix.

Re-trigger cubic</sub>

[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.

<sub>Reply with feedback, questions, or to request a fix.

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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.

Prompt for AI agents (unresolved issues)

Check if these issues are valid — if so, understand the root cause of each and fix them. If appropriate, use sub-agents to investigate and fix each issue separately.


<file name="document/graph-storage/src/attributes.rs">

<violation number="1" location="document/graph-storage/src/attributes.rs:113">
P2: `Priority` exposes its inner `f64`, so callers/deserialization can bypass the finite-value invariant enforced by `Priority::new`. Make invalid states unrepresentable by preventing direct construction and validating deserialization.</violation>
</file>

<file name="document/graph-storage/src/document.rs">

<violation number="1" location="document/graph-storage/src/document.rs:457">
P1: History iterator drops the root delta because `?` short-circuits before `Some(delta)`. This breaks history-based restoration when the relevant removal is at the root commit.</violation>
</file>

<file name="document/graph-storage/src/delta.rs">

<violation number="1" location="document/graph-storage/src/delta.rs:12">
P2: Diff generation is nondeterministic because it iterates `HashSet` differences/intersections. This makes identical state transitions produce different commit sequences and revision IDs across runs.</violation>
</file>

<file name="document/graph-storage/src/to_runtime.rs">

<violation number="1" location="document/graph-storage/src/to_runtime.rs:99">
P2: Per-network conversion does repeated full-map scans of `node_instances`, causing avoidable quadratic work on nested/large graphs. This can noticeably slow full rebuilds.</violation>

<violation number="2" location="document/graph-storage/src/to_runtime.rs:228">
P1: Node-reference remapping lacks a same-network validation guard. Cross-network references can be converted into wrong/dangling local runtime IDs instead of returning an error.</violation>
</file>

<sub>Reply with feedback, questions, or to request a fix.

Re-trigger cubic</sub>

[cubic-dev-ai]

P1: History iterator drops the root delta because ? short-circuits before Some(delta). This breaks history-based restoration when the relevant removal is at the root commit.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At document/graph-storage/src/document.rs, line 457:

<comment>History iterator drops the root delta because `?` short-circuits before `Some(delta)`. This breaks history-based restoration when the relevant removal is at the root commit.</comment>

<file context>
@@ -0,0 +1,480 @@
+	fn next(&mut self) -> Option<Self::Item> {
+		let delta = self.document.history.get(&self.parent_rev)?;
+		// First parent only for now. Local-chain walking (filter by author) is a follow-up.
+		self.parent_rev = *delta.parents.first()?;
+		Some(delta)
+	}
</file context>

[cubic-dev-ai]

P1: Node-reference remapping lacks a same-network validation guard. Cross-network references can be converted into wrong/dangling local runtime IDs instead of returning an error.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At document/graph-storage/src/to_runtime.rs, line 228:

<comment>Node-reference remapping lacks a same-network validation guard. Cross-network references can be converted into wrong/dangling local runtime IDs instead of returning an error.</comment>

<file context>
@@ -0,0 +1,277 @@
+
+fn convert_input(registry: &Registry, input: &NodeInput, input_attributes: &crate::Attributes) -> Result<GraphCraftNodeInput, ConversionError> {
+	Ok(match input {
+		NodeInput::Node { node_id, output_index } => {
+			let referenced = registry.node_instances.get(node_id).ok_or(ConversionError::NodeNotFound(*node_id))?;
+			let local_id = referenced.attributes.get(ORIGINAL_NODE_ID).and_then(|v| v.value.as_u64()).unwrap_or(*node_id);
</file context>

[cubic-dev-ai]

P2: Priority exposes its inner f64, so callers/deserialization can bypass the finite-value invariant enforced by Priority::new. Make invalid states unrepresentable by preventing direct construction and validating deserialization.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At document/graph-storage/src/attributes.rs, line 113:

<comment>`Priority` exposes its inner `f64`, so callers/deserialization can bypass the finite-value invariant enforced by `Priority::new`. Make invalid states unrepresentable by preventing direct construction and validating deserialization.</comment>

<file context>
@@ -0,0 +1,155 @@
+/// exact tie between two peers inserting at the same gap is broken by `PeerId` in [`SourceKey`].
+/// `f64` precision is ample for the short fallback chains resources carry in practice.
+#[derive(Copy, Clone, Debug, Serialize, Deserialize)]
+pub struct Priority(pub f64);
+
+impl Priority {
</file context>

[cubic-dev-ai]

P2: Diff generation is nondeterministic because it iterates HashSet differences/intersections. This makes identical state transitions produce different commit sequences and revision IDs across runs.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At document/graph-storage/src/delta.rs, line 12:

<comment>Diff generation is nondeterministic because it iterates `HashSet` differences/intersections. This makes identical state transitions produce different commit sequences and revision IDs across runs.</comment>

<file context>
@@ -0,0 +1,370 @@
+pub fn compute_deltas(from: &Registry, to: &Registry) -> Vec<RegistryDelta> {
+	let mut deltas = Vec::new();
+
+	let from_network_ids: HashSet<NetworkId> = from.networks.keys().copied().collect();
+	let to_network_ids: HashSet<NetworkId> = to.networks.keys().copied().collect();
+
</file context>

[cubic-dev-ai]

P2: Per-network conversion does repeated full-map scans of node_instances, causing avoidable quadratic work on nested/large graphs. This can noticeably slow full rebuilds.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At document/graph-storage/src/to_runtime.rs, line 99:

<comment>Per-network conversion does repeated full-map scans of `node_instances`, causing avoidable quadratic work on nested/large graphs. This can noticeably slow full rebuilds.</comment>

<file context>
@@ -0,0 +1,277 @@
+	}
+
+	let mut nodes: FxHashMap<RuntimeNodeId, DocumentNode> = FxHashMap::default();
+	for (&global_id, node) in registry.node_instances.iter().filter(|(_, node)| node.network == network_id) {
+		let local_id = node.attributes.get(ORIGINAL_NODE_ID).and_then(|v| v.value.as_u64()).unwrap_or(global_id);
+		let runtime_id = RuntimeNodeId(local_id);
</file context>