perf: fix memory leaks, optimize tracing logs, fix networking eof fragmentation bug in nvim-core and stub, and deduplicate json-rpc handlers

server/src/db.rs

@@ -0,0 +1,64 @@
+use std::path::Path;
+use std::sync::Arc;
+use redb::{Database, ReadableTable};
+use crate::store::STORE_TABLE;
+
+pub fn init_redb(base: &Path) -> Arc<Database> {
+    let redb_path = base.join("mcp_store.redb");
+    let db = Arc::new(redb::Database::create(&redb_path).expect("Failed to create redb database"));
+
+    // Ensure the table exists and migrate legacy JSON files
+    let write_txn = db.begin_write().expect("Failed to begin write txn on redb");
+    {
+        let mut table = write_txn
+            .open_table(STORE_TABLE)
+            .expect("Failed to open STORE_TABLE");
+
+        let stores = vec![
+            ("knowledge_graph_master", "knowledge_graph_master.json"),
+            ("audit_ledger", "audit_ledger.json"),
+            ("sticky_notes", "sticky_notes.json"),
+            ("tasks", "tasks.json"),
+            ("snippets", "snippets.json"),
+            ("adrs", "adrs.json"),
+            ("preferences", "preferences.json"),
+            ("error_fixes", "error_fixes.json"),
+            ("pinned_files", "pinned_files.json"),
+            ("session_summaries", "session_summaries.json"),
+            ("handoff_memos", "handoff_memos.json"),
+            ("env_fingerprints", "env_fingerprints.json"),
+            ("env_requirements", "env_requirements.json"),
+            ("milestones", "milestones.json"),
+            ("environments", "environments.json"),
+            ("pr_checklists", "pr_checklists.json"),
+            ("tech_debts", "tech_debts.json"),
+            ("gates", "gates.json"),
+            ("context_workspaces", "context_workspaces.json"),
+        ];
+
+        for (key, file_name) in stores.iter() {
+            if table
+                .get(*key)
+                .expect("Failed to read from table")
+                .is_none()
+            {
+                let json_path = base.join(file_name);
+                if json_path.exists()
+                    && let Ok(data) = std::fs::read(&json_path)
+                    && serde_json::from_slice::<serde_json::Value>(&data).is_ok()
+                {
+                    table
+                        .insert(*key, data.as_slice())
+                        .expect("Failed to insert migrated data");
+                    let _ = std::fs::rename(
+                        &json_path,
+                        json_path.with_extension("json.migrated"),
+                    );
+                }
+            }
+        }
+    }
+    write_txn.commit().expect("Failed to commit db migration");
+
+    db
+}