fix: enable LLM entity extraction + handle reasoning model output

Root causes of zero entity extraction:
1. IngestWorker used WikiLinkFallbackExtractor (wiki links only)
   Fix: Use LlmEntityExtractor when LLM_ENDPOINT is set
2. ExtractedEntity.entity_type vs LLM returning "type"
   Fix: serde alias "type" -> entity_type, default confidence
3. Reasoning models output <think>...</think> before JSON
   Fix: strip_thinking_tags() extracts JSON from response
4. Reflection verification crashes pipeline on parse failure
   Fix: graceful fallback, keep all entities if reflection fails

Tested with reasoning-predictor (qwen2.5:3b) via port-forward.

crates/mem-cli/src/ingest_worker.rs

@@ -2,7 +2,7 @@ use anyhow::Result;
 use mem_store::{MemoryL1, VectorStore, ChunkL0, EntityRepoOps, EdgeRepoOps};
 use mem_llm::EmbeddingsClient;
 use mem_ingest::ingest_pipeline::{IngestPipeline, Episode};
-use mem_ingest::entity_extractor::WikiLinkFallbackExtractor;
+use mem_ingest::entity_extractor::{WikiLinkFallbackExtractor, LlmEntityExtractor};
 use mem_ingest::fact_extractor::SimpleFactExtractor;
 use mem_ingest::contradiction_detector::ContradictionHandler;
 use sqlx::PgPool;
@@ -26,9 +26,16 @@ impl IngestWorker {
     ) -> Self {
         let vector_store = Arc::new(VectorStore::new(pool.clone()));
         
-        // Initialize extraction pipeline
+        // Initialize extraction pipeline — use LLM if LLM_ENDPOINT is set, else fallback to wiki links
         let entity_extractor: Arc<dyn mem_ingest::entity_extractor::EntityExtractor> = 
-            Arc::new(WikiLinkFallbackExtractor);
+            if std::env::var("LLM_ENDPOINT").is_ok() {
+                let model = std::env::var("LLM_MODEL").unwrap_or_else(|_| "qwen2.5:3b-instruct".to_string());
+                tracing::info!("Using LLM entity extractor: model={}", model);
+                Arc::new(LlmEntityExtractor::new(&model))
+            } else {
+                tracing::info!("LLM_ENDPOINT not set, using WikiLink fallback extractor");
+                Arc::new(WikiLinkFallbackExtractor)
+            };
         let fact_extractor: Arc<dyn mem_ingest::fact_extractor::FactExtractor> = 
             Arc::new(SimpleFactExtractor);
         let contradiction_detector = Arc::new(ContradictionHandler::default());

crates/mem-ingest/src/entity_extractor.rs

@@ -22,11 +22,15 @@ use tokio::sync::Mutex;
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ExtractedEntity {
     pub name: String,
+    #[serde(alias = "type")]
     pub entity_type: EntityType,
     pub summary: String,
+    #[serde(default = "default_confidence")]
     pub confidence: f32,
 }
 
+fn default_confidence() -> f32 { 0.8 }
+
 impl ExtractedEntity {
     /// Convert to domain model (Phase 1 type)
     pub fn to_domain(&self, project_id: &str) -> Entity {
@@ -62,6 +66,25 @@ impl LlmEntityExtractor {
 
     /// Parse extraction response JSON
     /// Format: { "entities": [{ "name": "...", "type": "...", "summary": "..." }, ...] }
+    /// Strip <think>...</think> tags from reasoning model output and extract JSON
+    fn strip_thinking_tags(text: &str) -> String {
+        let mut result = text.to_string();
+        // Remove <think>...</think> blocks
+        if let Some(start) = result.find("<think>") {
+            if let Some(end) = result.find("</think>") {
+                result = format!("{}{}", &result[..start], &result[end + 8..]);
+            }
+        }
+        // Try to find JSON object in remaining text
+        let trimmed = result.trim();
+        if let Some(start) = trimmed.find('{') {
+            if let Some(end) = trimmed.rfind('}') {
+                return trimmed[start..=end].to_string();
+            }
+        }
+        trimmed.to_string()
+    }
+
     fn parse_extraction(response: &str) -> Result<Vec<ExtractedEntity>> {
         #[derive(Deserialize)]
         struct Response {
@@ -146,12 +169,16 @@ impl LlmEntityExtractor {
         }
         
         let data: serde_json::Value = response.json().await?;
-        let content = data["choices"][0]["message"]["content"]
+        let raw_content = data["choices"][0]["message"]["content"]
             .as_str()
             .unwrap_or("{}")
             .to_string();
         
-        tracing::debug!("LLM response (via Authentik JWT): {}", content);
+        // Strip <think>...</think> tags from reasoning models
+        let content = Self::strip_thinking_tags(&raw_content);
+        
+        tracing::debug!("LLM raw response length={}, cleaned length={}", raw_content.len(), content.len());
+        tracing::debug!("LLM cleaned content: {}", content);
         Ok(content)
     }
     
@@ -233,14 +260,27 @@ Respond in JSON:
             );
 
             let reflection = if std::env::var("LLM_ENDPOINT").is_ok() {
-                self.call_llm_endpoint(&reflection_prompt).await.unwrap_or_else(|_| self.simulate_llm(&reflection_prompt).unwrap_or_default())
+                self.call_llm_endpoint(&reflection_prompt).await.unwrap_or_else(|e| {
+                    tracing::warn!("Reflection LLM call failed: {}, skipping verification", e);
+                    String::new()
+                })
             } else {
                 self.simulate_llm(&reflection_prompt)?
             };
-            let verified = Self::parse_reflection(&reflection)?;
 
-            // Filter: keep only entities marked present
-            entities.retain(|e| verified.iter().any(|(name, present)| name == &e.name && *present));
+            // If reflection succeeded, filter entities; otherwise keep all
+            if !reflection.is_empty() {
+                match Self::parse_reflection(&reflection) {
+                    Ok(verified) => {
+                        entities.retain(|e| verified.iter().any(|(name, present)| name == &e.name && *present));
+                    }
+                    Err(e) => {
+                        tracing::warn!("Reflection parse failed: {}, keeping all entities", e);
+                    }
+                }
+            } else {
+                tracing::info!("Reflection skipped, keeping {} unverified entities", entities.len());
+            }
 
             // Adjust confidence for reflected entities (slight penalty for needing verification)
             for entity in &mut entities {