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/tools.rs

@@ -151,7 +151,6 @@ pub struct VisualizeGraphTool {
     pub namespace: Option<String>,
 }
 
-
 /// Condense or summarize an entity's observations to reduce size.
 #[derive(Debug, Deserialize, Serialize, JsonSchema)]
 pub struct CondenseEntityTool {
@@ -327,13 +326,15 @@ pub struct VerifyAcceptanceCriteriaTool {
     pub proof: String,
 }
 
-/// Audit the knowledge graph to detect orphaned entities, compute name similarity for potential duplicate merges, and optionally auto-prune orphans.
+/// Audit the knowledge graph to detect orphaned entities, compute name similarity for potential duplicate merges, and optionally auto-prune orphans and stale file/symbol tombstones (ADR-0111).
 #[derive(Debug, Deserialize, Serialize, JsonSchema)]
 pub struct SweepGraphHealthTool {
     /// Optional flag to automatically prune orphaned nodes with 0 relations. Defaults to false.
     pub auto_prune_orphans: Option<bool>,
     /// Minimum string similarity threshold (0.0 to 1.0) to report duplicate entity pairs. Defaults to 0.8.
     pub similarity_threshold: Option<f32>,
+    /// Optional flag to prune stale entities whose file paths or symbols no longer exist on disk (ADR-0111). Defaults to false.
+    pub auto_prune_stale_files: Option<bool>,
 }
 
 /// Trace the causal provenance and historical lineage linking a task, ADR, git commit, code change, or error fix.