fix(p3): update stale Rust API consumers + fix KRaft flaky tests

- integration_test.rs: port to current OctadStore API (SimpleGraphStore,
  InMemoryProvenanceStore, InMemorySpatialStore, ConcreteOctadStore type
  alias, snapshot.embedding, OctadConfig::default(), two-arg search_similar)
- modality_benchmarks.rs: same API migration; add provenance/spatial Arc
  args to both InMemoryOctadStore::new() calls; OxiGraphStore → SimpleGraphStore
- kraft_node_test.exs: replace fixed Process.sleep assertions in two
  remove_server tests with poll_until/3 helper (polls every 50 ms, 2 s
  timeout) — eliminates pre-existing timeout failures under CI load

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: hyperpolymath

.machine_readable/6a2/STATE.a2ml

@@ -6,18 +6,18 @@
 [metadata]
 project = "nextgen-databases"
 version = "0.1.0"
-last-updated = "2026-04-11"
+last-updated = "2026-04-12"
 status = "active"
 
 [project-context]
 name = "nextgen-databases"
-completion-percentage = 55
-phase = "Phase 5 — Tropical Consonance + KRL Integration (P2 DONE)"
+completion-percentage = 62
+phase = "Phase 5 — Tropical Consonance + KRL Integration (P2 + P3 DONE)"
 
 [current-position]
-milestone = "verisim-modular-experiment tropical bridge v0.2 + bellman_ford proved"
-last-session = "2026-04-11"
-last-action = "P2: Tropical_Determinants.thy (sorry-free), TropicalDeterminant.jl, ProofOptimalAssignment VCL clause + 6 tests"
+milestone = "verisim-modular-experiment tropical bridge v0.2 + bellman_ford proved + P3 API fixes"
+last-session = "2026-04-12"
+last-action = "P3: integration_test.rs + modality_benchmarks.rs updated to current API; KRaft remove_server flaky tests fixed with poll_until helper"
 
 [tropical-bridge]
 status = "v0.2 — RI + RII live, RIII stub (KnotTheory.jl r3_simplify is no-op)"
@@ -47,13 +47,13 @@ cargo-bench-compile = "PASS (throughput_benchmarks.rs — no errors, no warnings
 gleam-smoke = "Written; requires compiled lith_nif.so to run connection/lifecycle tests"
 
 [blockers]
-- "Integration test (tests/integration_test.rs) uses old API — does not compile (pre-existing)"
-- "modality_benchmarks.rs uses old API — does not compile (pre-existing)"
+- "KRaft remove_server tests: timing-sensitive — mitigated with poll_until helper (was pre-existing timeout failure)"
 
 [route-to-mvp]
-next = "Update integration_test.rs to current API"
-then = "Update modality_benchmarks.rs to current API"
+next = "Promote verisim-modular-experiment impl/ to shippable verisim-core package"
+then = "Wire RIII neighbors when KnotTheory.jl gains live r3_simplify"
 
 [critical-next-actions]
-1 = "Update integration_test.rs to current API"
-2 = "Update modality_benchmarks.rs to current API"
+1 = "Promote impl/ to shippable verisim-core package"
+2 = "Wire _riii_neighbors when KnotTheory.jl gains live r3_simplify"
+3 = "Zig FFI port of VerisimCore per hyperpolymath standard"

verisimdb/benches/modality_benchmarks.rs

@@ -8,14 +8,16 @@ use tokio::runtime::Runtime;
 
 use verisim_document::{Document, DocumentStore, TantivyDocumentStore};
 use verisim_drift::{DriftDetector, DriftThresholds, DriftType};
-use verisim_graph::{GraphEdge, GraphNode, GraphObject, GraphStore, OxiGraphStore};
+use verisim_graph::{GraphEdge, GraphNode, GraphObject, GraphStore, SimpleGraphStore};
 use verisim_octad::{
     OctadConfig, OctadDocumentInput, OctadId, OctadInput, OctadSnapshot, OctadStore,
     OctadVectorInput, OctadSemanticInput, InMemoryOctadStore,
 };
+use verisim_provenance::InMemoryProvenanceStore;
 use verisim_semantic::{
     InMemorySemanticStore, ProofBlob, ProofType, SemanticStore, SemanticType,
 };
+use verisim_spatial::InMemorySpatialStore;
 use verisim_temporal::{InMemoryVersionStore, TemporalStore};
 use verisim_tensor::{InMemoryTensorStore, ReduceOp, Tensor, TensorStore};
 use verisim_vector::{DistanceMetric, Embedding, HnswConfig, HnswVectorStore, VectorStore};
@@ -142,7 +144,7 @@ fn bench_graph_operations(c: &mut Criterion) {
     let mut group = c.benchmark_group("graph");
 
     group.bench_function("insert_edge", |b| {
-        let store = OxiGraphStore::in_memory().unwrap();
+        let store = SimpleGraphStore::in_memory().unwrap();
         let mut counter = 0u64;
 
         b.to_async(&rt).iter(|| {
@@ -160,7 +162,7 @@ fn bench_graph_operations(c: &mut Criterion) {
     });
 
     // Pre-populate for query benchmark
-    let query_store = OxiGraphStore::in_memory().unwrap();
+    let query_store = SimpleGraphStore::in_memory().unwrap();
     let query_node = GraphNode::new("https://example.org/hub");
     rt.block_on(async {
         for i in 0..100 {
@@ -190,12 +192,14 @@ fn bench_octad_operations(c: &mut Criterion) {
     let rt = Runtime::new().unwrap();
     let mut group = c.benchmark_group("octad");
 
-    let graph_store = Arc::new(OxiGraphStore::in_memory().unwrap());
-    let vector_store = Arc::new(HnswVectorStore::new(384, DistanceMetric::Cosine, HnswConfig::default()));
-    let document_store = Arc::new(TantivyDocumentStore::in_memory().unwrap());
-    let tensor_store = Arc::new(InMemoryTensorStore::new());
-    let semantic_store = Arc::new(InMemorySemanticStore::new());
+    let graph_store     = Arc::new(SimpleGraphStore::in_memory().unwrap());
+    let vector_store    = Arc::new(HnswVectorStore::new(384, DistanceMetric::Cosine, HnswConfig::default()));
+    let document_store  = Arc::new(TantivyDocumentStore::in_memory().unwrap());
+    let tensor_store    = Arc::new(InMemoryTensorStore::new());
+    let semantic_store  = Arc::new(InMemorySemanticStore::new());
     let temporal_store: Arc<InMemoryVersionStore<OctadSnapshot>> = Arc::new(InMemoryVersionStore::new());
+    let provenance_store = Arc::new(InMemoryProvenanceStore::new());
+    let spatial_store   = Arc::new(InMemorySpatialStore::new());
 
     let config = OctadConfig::default();
 
@@ -207,6 +211,8 @@ fn bench_octad_operations(c: &mut Criterion) {
         tensor_store,
         semantic_store,
         temporal_store,
+        provenance_store,
+        spatial_store,
     );
 
     group.bench_function("create_octad", |b| {
@@ -300,12 +306,14 @@ fn bench_cross_modal_query(c: &mut Criterion) {
     let rt = Runtime::new().unwrap();
     let mut group = c.benchmark_group("cross_modal");
 
-    let graph_store = Arc::new(OxiGraphStore::in_memory().unwrap());
-    let vector_store = Arc::new(HnswVectorStore::new(384, DistanceMetric::Cosine, HnswConfig::default()));
-    let document_store = Arc::new(TantivyDocumentStore::in_memory().unwrap());
-    let tensor_store = Arc::new(InMemoryTensorStore::new());
-    let semantic_store = Arc::new(InMemorySemanticStore::new());
+    let graph_store     = Arc::new(SimpleGraphStore::in_memory().unwrap());
+    let vector_store    = Arc::new(HnswVectorStore::new(384, DistanceMetric::Cosine, HnswConfig::default()));
+    let document_store  = Arc::new(TantivyDocumentStore::in_memory().unwrap());
+    let tensor_store    = Arc::new(InMemoryTensorStore::new());
+    let semantic_store  = Arc::new(InMemorySemanticStore::new());
     let temporal_store: Arc<InMemoryVersionStore<OctadSnapshot>> = Arc::new(InMemoryVersionStore::new());
+    let provenance_store = Arc::new(InMemoryProvenanceStore::new());
+    let spatial_store   = Arc::new(InMemorySpatialStore::new());
 
     let config = OctadConfig::default();
 
@@ -317,6 +325,8 @@ fn bench_cross_modal_query(c: &mut Criterion) {
         tensor_store,
         semantic_store,
         temporal_store,
+        provenance_store,
+        spatial_store,
     );
 
     // Create 1000 octads with multiple modalities

verisimdb/elixir-orchestration/test/verisim/consensus/kraft_node_test.exs

@@ -34,6 +34,28 @@ defmodule VeriSim.Consensus.KRaftNodeTest do
     :exit, _ -> :ok
   end
 
+  # Poll `fun` every `interval_ms` ms until it returns a truthy value, or
+  # fail after `timeout_ms` ms have elapsed.  Used for membership-change
+  # assertions where the commit + apply cycle can be slower under CI load.
+  defp poll_until(fun, timeout_ms \\ 2_000, interval_ms \\ 50) do
+    deadline = System.monotonic_time(:millisecond) + timeout_ms
+
+    Enum.reduce_while(Stream.repeatedly(fn -> :poll end), nil, fn _, _acc ->
+      if fun.() do
+        {:halt, :ok}
+      else
+        remaining = deadline - System.monotonic_time(:millisecond)
+
+        if remaining <= 0 do
+          {:halt, :timeout}
+        else
+          Process.sleep(min(interval_ms, remaining))
+          {:cont, nil}
+        end
+      end
+    end)
+  end
+
   describe "single-node leader election" do
     test "node with 0 peers becomes leader within 500ms" do
       node_id = "solo-#{System.unique_integer([:positive])}"
@@ -179,13 +201,24 @@ defmodule VeriSim.Consensus.KRaftNodeTest do
 
       # Add then remove
       {:ok, _} = KRaftNode.add_server(node_id, "ephemeral-peer", [])
-      Process.sleep(100)
+
+      # Wait for add to be committed before issuing remove
+      :ok =
+        poll_until(fn ->
+          members = get_in(KRaftNode.registry(node_id), [:config, :members]) || []
+          "ephemeral-peer" in members
+        end)
+
       {:ok, _} = KRaftNode.remove_server(node_id, "ephemeral-peer")
-      Process.sleep(100)
 
-      registry = KRaftNode.registry(node_id)
-      members = get_in(registry, [:config, :members]) || []
-      refute "ephemeral-peer" in members
+      # Poll until the commit + state-machine apply removes the member
+      result =
+        poll_until(fn ->
+          members = get_in(KRaftNode.registry(node_id), [:config, :members]) || []
+          "ephemeral-peer" not in members
+        end)
+
+      assert result == :ok, "ephemeral-peer was not removed from registry within 2 s"
 
       stop_kraft(pid)
     end
@@ -200,9 +233,20 @@ defmodule VeriSim.Consensus.KRaftNodeTest do
       leader_pid = start_kraft(leader_id, [follower_id])
       follower_pid = start_kraft(follower_id, [leader_id])
 
-      Process.sleep(1_000)
+      # Poll until exactly one leader has been elected (up to 3 s under CI load)
+      result =
+        poll_until(
+          fn ->
+            roles = Enum.map([leader_id, follower_id], &KRaftNode.diagnostics(&1).role)
+            Enum.count(roles, &(&1 == :leader)) == 1
+          end,
+          3_000,
+          100
+        )
+
+      assert result == :ok, "Cluster did not elect a leader within 3 s"
 
-      # Find which one is leader
+      # Find which node is actually the leader
       leader_diag = KRaftNode.diagnostics(leader_id)
       {actual_leader, actual_follower, actual_follower_pid} =
         if leader_diag.role == :leader do
@@ -213,11 +257,19 @@ defmodule VeriSim.Consensus.KRaftNodeTest do
 
       # Remove the follower via the leader
       {:ok, _} = KRaftNode.remove_server(actual_leader, actual_follower)
-      Process.sleep(200)
 
-      # Leader's peer count should now be 0 (follower removed from peers)
-      diag = KRaftNode.diagnostics(actual_leader)
-      assert diag.peer_count == 0
+      # Poll until the leader's peer list has been updated (commit + apply)
+      remove_result =
+        poll_until(
+          fn ->
+            KRaftNode.diagnostics(actual_leader).peer_count == 0
+          end,
+          2_000,
+          50
+        )
+
+      assert remove_result == :ok,
+             "Leader peer_count did not drop to 0 within 2 s after remove_server"
 
       stop_kraft(leader_pid)
       stop_kraft(follower_pid)