fix(sight): preserve user config on schema migration

src/agentsight/src/config.rs

@@ -534,19 +534,45 @@ pub fn ensure_default_agents_config(path: &Path) -> anyhow::Result<()> {
         return Ok(());
     }
 
+    // Shallow-merge: start from the embedded default, overlay all top-level
+    // keys the user has set (except schema_version itself), then bump version.
+    // This preserves user customizations (cmdline rules, https rules,
+    // codex_offsets, feature overrides) while adding any NEW sections from the
+    // default that the old config was missing. Fixes #1496 — the previous
+    // implementation did a destructive overwrite that silently lost user data.
+    let mut base: serde_json::Value = serde_json::from_str(DEFAULT_AGENTS_JSON)
+        .expect("embedded DEFAULT_AGENTS_JSON must be valid");
+    let user: serde_json::Value =
+        serde_json::from_str(&content).expect("JSON validity already confirmed above");
+
+    if let (Some(base_obj), Some(user_obj)) = (base.as_object_mut(), user.as_object()) {
+        for (key, value) in user_obj {
+            if key == "schema_version" {
+                continue;
+            }
+            base_obj.insert(key.clone(), value.clone());
+        }
+        base_obj.insert(
+            "schema_version".to_string(),
+            serde_json::Value::Number(CURRENT_SCHEMA_VERSION.into()),
+        );
+    }
+
+    let merged = serde_json::to_string_pretty(&base).expect("merged config must serialize");
+
     let backup = {
         let ts = std::time::SystemTime::now()
             .duration_since(std::time::UNIX_EPOCH)
             .map(|d| d.as_secs())
             .unwrap_or(0);
         path.with_extension(format!("json.bak.{ts}"))
     };
-    std::fs::rename(path, &backup)
+    std::fs::copy(path, &backup)
         .with_context(|| format!("Failed to back up {path:?} to {backup:?}"))?;
-    std::fs::write(path, DEFAULT_AGENTS_JSON)
-        .with_context(|| format!("Failed to write updated agents config to {path:?}"))?;
+    std::fs::write(path, &merged)
+        .with_context(|| format!("Failed to write merged config to {path:?}"))?;
     log::info!(
-        "Config schema_version {:?} < {}, overwrote {path:?} (backup at {backup:?})",
+        "Config schema_version {:?} < {}, merged user config with defaults at {path:?} (backup at {backup:?})",
         on_disk_version,
         CURRENT_SCHEMA_VERSION
     );
@@ -2141,4 +2167,72 @@ mod tests {
             .collect();
         assert!(backups.is_empty());
     }
+
+    #[test]
+    fn ensure_default_agents_config_preserves_user_cmdline_rules_on_merge() {
+        // Regression for #1496: when migrating a valid v1 config to v2, user
+        // customizations (cmdline rules, etc.) must survive — not be overwritten
+        // with the embedded default. Discriminating: reverting to the old
+        // overwrite logic would lose "MyCustomAgent" and fail this test.
+        let dir = unique_temp_dir();
+        let path = dir.join("agentsight.json");
+        let user_config = r#"{
+            "schema_version": 1,
+            "cmdline": {
+                "allow": [
+                    {"rule": ["*mycustomagent*"], "agent_name": "MyCustomAgent"}
+                ],
+                "deny": [{"rule": ["*noisy*"]}]
+            },
+            "https": [{"rule": ["custom.api.example.com"]}]
+        }"#;
+        std::fs::write(&path, user_config).unwrap();
+        ensure_default_agents_config(&path).unwrap();
+        let result = std::fs::read_to_string(&path).unwrap();
+        // User's custom agent rule must survive migration
+        assert!(
+            result.contains("MyCustomAgent"),
+            "user cmdline rule lost during migration: {result}"
+        );
+        assert!(
+            result.contains("custom.api.example.com"),
+            "user https rule lost during migration: {result}"
+        );
+        assert!(
+            result.contains("*noisy*"),
+            "user deny rule lost during migration: {result}"
+        );
+        // schema_version must be bumped to current
+        let migrated: serde_json::Value = serde_json::from_str(&result).unwrap();
+        assert_eq!(
+            migrated["schema_version"].as_u64().unwrap() as u32,
+            CURRENT_SCHEMA_VERSION
+        );
+    }
+
+    #[test]
+    fn ensure_default_agents_config_adds_missing_sections_on_merge() {
+        // A v1 config that only has cmdline should gain features/runtime_limits
+        // from the default after migration — verifies additive merge.
+        let dir = unique_temp_dir();
+        let path = dir.join("agentsight.json");
+        let minimal_v1 = r#"{
+            "cmdline": {"allow": [{"rule": ["*test*"], "agent_name": "Test"}]}
+        }"#;
+        std::fs::write(&path, minimal_v1).unwrap();
+        ensure_default_agents_config(&path).unwrap();
+        let result = std::fs::read_to_string(&path).unwrap();
+        let migrated: serde_json::Value = serde_json::from_str(&result).unwrap();
+        // New sections from default must be present
+        assert!(
+            migrated.get("features").is_some(),
+            "features section not added from default"
+        );
+        assert!(
+            migrated.get("runtime_limits").is_some(),
+            "runtime_limits section not added from default"
+        );
+        // User's original rule must still be there
+        assert!(result.contains("Test"), "user rule lost");
+    }
 }