feat: v2.0.4 "Deep Reference" — cognitive reasoning engine + 10 bug fixes

New features:
- deep_reference tool (#22): 8-stage cognitive reasoning pipeline with FSRS-6
  trust scoring, intent classification (FactCheck/Timeline/RootCause/Comparison/
  Synthesis), spreading activation expansion, temporal supersession, trust-weighted
  contradiction analysis, relation assessment, dream insight integration, and
  algorithmic reasoning chain generation — all without calling an LLM
- cross_reference (#23): backward-compatible alias for deep_reference
- retrieval_mode parameter on search (precise/balanced/exhaustive)
- get_batch action on memory tool (up to 20 IDs per call)
- Token budget raised from 10K to 100K on search + session_context
- Dates (createdAt/updatedAt) on all search results and session_context lines

Bug fixes (GitHub Issue #25 — all 10 resolved):
- state_transitions empty: wired record_memory_access into strengthen_batch
- chain/bridges no storage fallback: added with edge deduplication
- knowledge_edges dead schema: documented as deprecated
- insights not persisted from dream: wired save_insight after generation
- find_duplicates threshold dropped: serde alias fix
- search min_retention ignored: serde aliases for snake_case params
- intention time triggers null: removed dead trigger_at embedding
- changelog missing dreams: added get_dream_history + event integration
- phantom Related IDs: clarified message text
- fsrs_cards empty: documented as harmless dead schema

Security hardening:
- HTTP transport CORS: permissive() → localhost-only
- Auth token panic guard: &token[..8] → safe min(8) slice
- UTF-8 boundary fix: floor_char_boundary on content truncation
- All unwrap() removed from HTTP transport (unwrap_or_else fallback)
- Dream memory_count capped at 500 (prevents O(N²) hang)
- Dormant state threshold aligned (0.3 → 0.4)

Stats: 23 tools, 758 tests, 0 failures, 0 warnings, 0 unwraps in production

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

crates/vestige-core/src/advanced/mod.rs

@@ -29,7 +29,7 @@ pub mod speculative;
 
 // Re-exports for convenient access
 pub use adaptive_embedding::{AdaptiveEmbedder, ContentType, EmbeddingStrategy, Language};
-pub use chains::{ChainStep, ConnectionType, MemoryChainBuilder, MemoryPath, ReasoningChain};
+pub use chains::{ChainStep, Connection, ConnectionType, MemoryChainBuilder, MemoryNode, MemoryPath, ReasoningChain};
 pub use compression::{CompressedMemory, CompressionConfig, CompressionStats, MemoryCompressor};
 pub use cross_project::{
     ApplicableKnowledge, CrossProjectLearner, ProjectContext, UniversalPattern,

crates/vestige-core/src/storage/migrations.rs

@@ -315,7 +315,10 @@ const MIGRATION_V4_UP: &str = r#"
 -- TEMPORAL KNOWLEDGE GRAPH (Like Zep's Graphiti)
 -- ============================================================================
 
--- Knowledge edges for temporal reasoning
+-- DEPRECATED (v2.1.0): knowledge_edges is unused. All graph edges use
+-- memory_connections (migration V3). This table was designed for bi-temporal
+-- edge support but was never wired. Retained for schema compatibility with
+-- existing databases. Do NOT add queries against this table.
 CREATE TABLE IF NOT EXISTS knowledge_edges (
     id TEXT PRIMARY KEY,
     source_id TEXT NOT NULL,

crates/vestige-core/src/storage/sqlite.rs

@@ -227,6 +227,7 @@ impl Storage {
             .lock()
             .map_err(|_| StorageError::Init("Vector index lock poisoned".to_string()))?;
 
+        let mut load_failures = 0u32;
         for (node_id, embedding_bytes) in embeddings {
             if let Some(embedding) = Embedding::from_bytes(&embedding_bytes) {
                 // Handle Matryoshka migration: old 768-dim → truncate to 256-dim
@@ -236,10 +237,14 @@ impl Storage {
                     embedding.vector
                 };
                 if let Err(e) = index.add(&node_id, &vector) {
+                    load_failures += 1;
                     tracing::warn!("Failed to load embedding for {}: {}", node_id, e);
                 }
             }
         }
+        if load_failures > 0 {
+            tracing::error!(count = load_failures, "Vector index: {} embeddings failed to load", load_failures);
+        }
 
         Ok(())
     }
@@ -399,7 +404,11 @@ impl Storage {
                     superseded_id: None,
                     similarity: None,
                     prediction_error: Some(prediction_error),
-                    reason: format!("Created new memory: {:?}. Related: {:?}", reason, related_memory_ids),
+                    reason: if related_memory_ids.is_empty() {
+                        format!("Created new memory: {:?}", reason)
+                    } else {
+                        format!("Created new memory: {:?}. Semantically similar (not linked): {:?}", reason, related_memory_ids)
+                    },
                 })
             }
             GateDecision::Update { target_id, similarity, update_type, prediction_error } => {
@@ -667,7 +676,13 @@ impl Storage {
     /// Convert a row to KnowledgeNode
     fn row_to_node(row: &rusqlite::Row) -> rusqlite::Result<KnowledgeNode> {
         let tags_json: String = row.get("tags")?;
-        let tags: Vec<String> = serde_json::from_str(&tags_json).unwrap_or_default();
+        let tags: Vec<String> = match serde_json::from_str(&tags_json) {
+            Ok(t) => t,
+            Err(e) => {
+                tracing::warn!(raw = %tags_json, "Failed to deserialize tags JSON, using empty: {}", e);
+                Vec::new()
+            }
+        };
 
         let created_at: String = row.get("created_at")?;
         let updated_at: String = row.get("updated_at")?;
@@ -955,6 +970,8 @@ impl Storage {
     pub fn strengthen_batch_on_access(&self, ids: &[&str]) -> Result<()> {
         for id in ids {
             self.strengthen_on_access(id)?;
+            // Also record access in memory_states for audit trail (Bug #1 fix)
+            let _ = self.record_memory_access(id);
         }
         Ok(())
     }
@@ -3223,6 +3240,42 @@ impl Storage {
         }))
     }
 
+    /// Get dream history (most recent first)
+    pub fn get_dream_history(&self, limit: i32) -> Result<Vec<DreamHistoryRecord>> {
+        let reader = self.reader.lock()
+            .map_err(|_| StorageError::Init("Reader lock poisoned".into()))?;
+        let mut stmt = reader.prepare(
+            "SELECT dreamed_at, duration_ms, memories_replayed, connections_found,
+                    insights_generated, memories_strengthened, memories_compressed,
+                    phase_nrem1_ms, phase_nrem3_ms, phase_rem_ms, phase_integration_ms,
+                    summaries_generated, emotional_memories_processed, creative_connections_found
+             FROM dream_history ORDER BY dreamed_at DESC LIMIT ?1"
+        )?;
+        let records = stmt.query_map(params![limit], |row| {
+            let dreamed_at_str: String = row.get(0)?;
+            let dreamed_at = DateTime::parse_from_rfc3339(&dreamed_at_str)
+                .map(|dt| dt.with_timezone(&Utc))
+                .unwrap_or_else(|_| Utc::now());
+            Ok(DreamHistoryRecord {
+                dreamed_at,
+                duration_ms: row.get(1)?,
+                memories_replayed: row.get(2)?,
+                connections_found: row.get(3)?,
+                insights_generated: row.get(4)?,
+                memories_strengthened: row.get(5)?,
+                memories_compressed: row.get(6)?,
+                phase_nrem1_ms: row.get(7)?,
+                phase_nrem3_ms: row.get(8)?,
+                phase_rem_ms: row.get(9)?,
+                phase_integration_ms: row.get(10)?,
+                summaries_generated: row.get(11)?,
+                emotional_memories_processed: row.get(12)?,
+                creative_connections_found: row.get(13)?,
+            })
+        })?.collect::<std::result::Result<Vec<_>, _>>()?;
+        Ok(records)
+    }
+
     /// Count memories created since a given timestamp
     pub fn count_memories_since(&self, since: DateTime<Utc>) -> Result<i64> {
         let reader = self.reader.lock()