feat(adr): implement ADR-0109, ADR-0110, and ADR-0111

- ADR-0109: Incremental Background AST Indexing & Differential Graph Updates via Tree-Sitter
- ADR-0110: Real-Time SSE Live Activity & Log Stream (/api/events/stream)
- ADR-0111: Automated Stale Symbol Pruning & Graph Tombstoning (sweep_graph_health auto_prune_stale_files)

server/src/handlers/graph.rs

@@ -1044,9 +1044,11 @@ impl McpTool for SweepGraphHealthHandler {
     async fn execute(&self, args: Value, state: Arc<MemoryState>) -> crate::error::Result<String> {
         let req: SweepGraphHealthTool = serde_json::from_value(args).map_err(|e| e.to_string())?;
         let auto_prune = req.auto_prune_orphans.unwrap_or(false);
+        let auto_prune_stale = req.auto_prune_stale_files.unwrap_or(false);
 
         let mut orphans = Vec::new();
         let mut duplicates = Vec::new();
+        let mut stale_entities = Vec::new();
 
         state.modify_graph(|g| {
             // 1. Identify Orphans
@@ -1062,12 +1064,31 @@ impl McpTool for SweepGraphHealthHandler {
                 }
             }
 
+            // ADR-0111: Automated Stale Symbol Pruning & Graph Tombstoning
+            for (name, entity) in g.entities.iter() {
+                if entity.entity_type == "File" || name.contains(".rs") || name.contains(".ts") || name.contains(".js") || name.contains(".py") {
+                    let check_path = entity.file_path.as_deref().unwrap_or(name.as_str());
+                    // Strip any symbol qualifiers like File::symbol
+                    let base_file = check_path.split("::").next().unwrap_or(check_path);
+                    if (base_file.contains('/') || base_file.contains('\\') || base_file.ends_with(".rs") || base_file.ends_with(".ts")) && !std::path::Path::new(base_file).exists() {
+                        stale_entities.push(name.clone());
+                    }
+                }
+            }
+
             if auto_prune {
                 for orphan in &orphans {
                     g.entities.remove(orphan);
                 }
             }
 
+            if auto_prune_stale {
+                for stale in &stale_entities {
+                    g.entities.remove(stale);
+                    g.relations.retain(|r| &r.from != stale && &r.to != stale);
+                }
+            }
+
             // 2. Compute similarity pairs for duplicate detection using pre-computed lowercase names
             let names: Vec<_> = g.entities.keys().cloned().collect();
             let lower_names: Vec<String> = names.iter().map(|n| n.to_lowercase()).collect();
@@ -1092,8 +1113,10 @@ impl McpTool for SweepGraphHealthHandler {
         let report = serde_json::json!({
             "orphaned_entities": orphans,
             "orphans_pruned": auto_prune,
+            "stale_entities": stale_entities,
+            "stale_pruned": auto_prune_stale,
             "potential_duplicates": duplicates,
-            "health_score": if orphans.is_empty() && duplicates.is_empty() { "100%" } else { "Needs Maintenance" }
+            "health_score": if orphans.is_empty() && duplicates.is_empty() && stale_entities.is_empty() { "100%" } else { "Needs Maintenance" }
         });
 
         Ok(serde_json::to_string_pretty(&report)?)