diff --git a/crates/hk-desktop/src/commands/install.rs b/crates/hk-desktop/src/commands/install.rs
index a4664ce..6c4e50a 100644
--- a/crates/hk-desktop/src/commands/install.rs
+++ b/crates/hk-desktop/src/commands/install.rs
@@ -17,6 +17,27 @@ pub enum ScanResult {
     NoSkills,
 }
 
+/// Names of agents that are both detected on disk and enabled in settings —
+/// the targets an "install to all detected agents" fallback should use when the
+/// caller passes no explicit list. Mirrors the frontend, which only offers
+/// detected + enabled agents as install targets.
+fn enabled_detected_agents(
+    store: &hk_core::store::Store,
+    adapters: &[Box<dyn hk_core::adapter::AgentAdapter>],
+) -> Vec<String> {
+    adapters
+        .iter()
+        .filter(|a| {
+            a.detect()
+                && store
+                    .get_agent_setting(a.name())
+                    .map(|(_, enabled)| enabled)
+                    .unwrap_or(true)
+        })
+        .map(|a| a.name().to_string())
+        .collect()
+}
+
 #[tauri::command]
 pub async fn list_hermes_categories(
     state: State<'_, AppState>,
@@ -67,11 +88,7 @@ pub async fn install_from_local(
         });
 
         let agents: Vec<String> = if target_agents.is_empty() {
-            adapters
-                .iter()
-                .filter(|a| a.detect())
-                .map(|a| a.name().to_string())
-                .collect()
+            enabled_detected_agents(&store.lock(), &adapters)
         } else {
             target_agents
         };
@@ -270,10 +287,9 @@ pub async fn scan_git_repo(
                 // Auto-install single skill
                 let agents = if target_agents.is_empty() {
                     vec![
-                        adapters
-                            .iter()
-                            .find(|a| a.detect())
-                            .map(|a| a.name().to_string())
+                        enabled_detected_agents(&store_clone.lock(), &adapters)
+                            .into_iter()
+                            .next()
                             .ok_or_else(|| HkError::NotFound("No detected agent found".into()))?,
                     ]
                 } else {
diff --git a/src/App.tsx b/src/App.tsx
index d6902ca..7dc45e0 100644
--- a/src/App.tsx
+++ b/src/App.tsx
@@ -56,20 +56,32 @@ export default function App() {
     return () => mq.removeEventListener("change", onChange);
   }, [mode]);
 
-  // Keep "Detected only" honest over time: undetected agents must stay disabled
-  // — including ones added by a later app update while the user stays in this
-  // mode (the per-click handler in Settings can't catch those). Reconcile
-  // whenever the agent list or visibility changes. Converges: once disabled an
-  // agent is no longer "enabled", so the next run finds nothing to do.
+  // Keep "Detected only" honest over time, in both directions: disable agents
+  // that aren't detected, and re-enable ones we disabled once they're detected
+  // again (e.g. their config dir was removed then restored). Reconcile whenever
+  // the agent list or visibility changes. Converges: a disabled agent is no
+  // longer "enabled" and a re-enabled one leaves the snapshot, so the next run
+  // finds nothing to do.
   useEffect(() => {
     if (agentVisibility !== "detected") return;
-    const stray = agents
+    const { autoDisabledAgents, setAutoDisabledAgents } = useUIStore.getState();
+    const snapshot = new Set(autoDisabledAgents);
+
+    const toDisable = agents
       .filter((a) => !a.detected && a.enabled)
       .map((a) => a.name);
-    if (stray.length === 0) return;
-    useAgentStore.getState().setEnabledBulk(stray, false);
-    const { autoDisabledAgents, setAutoDisabledAgents } = useUIStore.getState();
-    setAutoDisabledAgents([...new Set([...autoDisabledAgents, ...stray])]);
+    const toReEnable = agents
+      .filter((a) => a.detected && !a.enabled && snapshot.has(a.name))
+      .map((a) => a.name);
+    if (toDisable.length === 0 && toReEnable.length === 0) return;
+
+    const setEnabledBulk = useAgentStore.getState().setEnabledBulk;
+    if (toDisable.length > 0) setEnabledBulk(toDisable, false);
+    if (toReEnable.length > 0) setEnabledBulk(toReEnable, true);
+
+    for (const n of toDisable) snapshot.add(n);
+    for (const n of toReEnable) snapshot.delete(n);
+    setAutoDisabledAgents([...snapshot]);
   }, [agents, agentVisibility]);
 
   // Check for updates on startup (non-blocking, silent failure).
@@ -91,6 +103,10 @@ export default function App() {
       api
         .scanAndSync()
         .then(() => {
+          // Refresh agent detection too (detect() is live), so an agent dir
+          // added/removed outside the app shows up on focus — not just
+          // extensions.
+          useAgentStore.getState().fetch();
           fetchExtensions();
           loadCachedAudit();
         })
diff --git a/src/components/agents/agent-detail.tsx b/src/components/agents/agent-detail.tsx
index f5b768f..b1153ef 100644
--- a/src/components/agents/agent-detail.tsx
+++ b/src/components/agents/agent-detail.tsx
@@ -12,8 +12,8 @@ import {
   type ExtensionCounts,
 } from "@/lib/types";
 import { useAgentConfigStore } from "@/stores/agent-config-store";
+import { useAgentStore } from "@/stores/agent-store";
 import { useExtensionStore } from "@/stores/extension-store";
-import { useUIStore } from "@/stores/ui-store";
 import { ConfigSection } from "./config-section";
 import { ExtensionsSummaryCard } from "./extensions-summary-card";
 import { SectionAnchorRail } from "./section-anchor-rail";
@@ -27,7 +27,7 @@ export function AgentDetail() {
   const allExtensions = useExtensionStore((s) => s.extensions);
   const { scope } = useScope();
   const agent = agentDetails.find((a) => a.name === selectedAgent);
-  const agentVisibility = useUIStore((s) => s.agentVisibility);
+  const agents = useAgentStore((s) => s.agents);
   const [showAddForm, setShowAddForm] = useState(false);
   const [customPath, setCustomPath] = useState("");
 
@@ -64,7 +64,7 @@ export function AgentDetail() {
   if (!agent) {
     return (
       <div className="flex flex-1 items-center justify-center text-muted-foreground text-sm">
-        {agentVisibility === "detected" && !agentDetails.some((a) => a.detected)
+        {agents.length > 0 && !agents.some((a) => a.enabled)
           ? t("list.noDetected")
           : t("detail.selectAgent")}
       </div>
diff --git a/src/components/agents/agent-list.tsx b/src/components/agents/agent-list.tsx
index b808c4e..6e6da61 100644
--- a/src/components/agents/agent-list.tsx
+++ b/src/components/agents/agent-list.tsx
@@ -25,7 +25,6 @@ import type { AgentDetail } from "@/lib/types";
 import { agentDisplayName } from "@/lib/types";
 import { useAgentConfigStore } from "@/stores/agent-config-store";
 import { useAgentStore } from "@/stores/agent-store";
-import { useUIStore } from "@/stores/ui-store";
 
 function SortableAgentItem({
   agent,
@@ -100,7 +99,7 @@ export function AgentList() {
   const selectAgent = useAgentConfigStore((s) => s.selectAgent);
   const agentOrder = useAgentStore((s) => s.agentOrder);
   const reorderAgents = useAgentStore((s) => s.reorderAgents);
-  const agentVisibility = useUIStore((s) => s.agentVisibility);
+  const agents = useAgentStore((s) => s.agents);
 
   const sorted = useMemo(
     () =>
@@ -112,36 +111,37 @@ export function AgentList() {
     [agentDetails, agentOrder],
   );
 
+  // A disabled agent (including ones "Detected only" auto-disabled) is hidden
+  // from the sidebar. AgentDetail doesn't carry enabled state, so cross-
+  // reference the agent store; default to visible when an agent is unknown
+  // (store not loaded yet) so the list never flashes empty.
+  const disabledNames = useMemo(
+    () => new Set(agents.filter((a) => !a.enabled).map((a) => a.name)),
+    [agents],
+  );
+
   const visible = useMemo(
-    () =>
-      agentVisibility === "detected"
-        ? sorted.filter((a) => a.detected)
-        : sorted,
-    [sorted, agentVisibility],
+    () => sorted.filter((a) => !disabledNames.has(a.name)),
+    [sorted, disabledNames],
   );
 
   const hidden = useMemo(
     () =>
       new Set(
-        agentVisibility === "detected"
-          ? sorted.filter((a) => !a.detected).map((a) => a.name)
-          : [],
+        sorted.filter((a) => disabledNames.has(a.name)).map((a) => a.name),
       ),
-    [sorted, agentVisibility],
+    [sorted, disabledNames],
   );
 
+  // Keep the selection on a visible agent — if the selected one gets hidden
+  // (disabled), fall back to the first visible, or clear it.
   useEffect(() => {
-    if (agentVisibility !== "detected") return;
     if (!selectedAgent) return;
     const isSelectedVisible = visible.some((a) => a.name === selectedAgent);
     if (!isSelectedVisible) {
-      if (visible.length > 0) {
-        selectAgent(visible[0].name);
-      } else {
-        selectAgent(null);
-      }
+      selectAgent(visible.length > 0 ? visible[0].name : null);
     }
-  }, [agentVisibility, visible, selectedAgent, selectAgent]);
+  }, [visible, selectedAgent, selectAgent]);
 
   const sensors = useSensors(
     useSensor(PointerSensor, { activationConstraint: { distance: 5 } }),
diff --git a/src/components/extensions/extension-detail.tsx b/src/components/extensions/extension-detail.tsx
index a61b289..2d67f5a 100644
--- a/src/components/extensions/extension-detail.tsx
+++ b/src/components/extensions/extension-detail.tsx
@@ -479,7 +479,7 @@ export function ExtensionDetail() {
           group.kind === "cli") &&
           (() => {
             const detectedAgents = sortAgents(
-              agents.filter((a) => a.detected),
+              agents.filter((a) => a.detected && a.enabled),
               agentOrder,
             );
             const AGENTS_WITHOUT_HOOKS = new Set(["antigravity", "opencode"]);
diff --git a/src/components/extensions/extension-filters.tsx b/src/components/extensions/extension-filters.tsx
index ce5a2ae..7d62dd9 100644
--- a/src/components/extensions/extension-filters.tsx
+++ b/src/components/extensions/extension-filters.tsx
@@ -7,7 +7,6 @@ import { isWeb as web, webSelectStyle } from "@/lib/web-select";
 import { useAgentStore } from "@/stores/agent-store";
 import { useExtensionStore } from "@/stores/extension-store";
 import { useScopeStore } from "@/stores/scope-store";
-import { useUIStore } from "@/stores/ui-store";
 
 const TAG_COLORS = [
   "bg-primary/10 text-primary",
@@ -87,16 +86,13 @@ export function ExtensionFilters() {
   }, [grouped, extensions, scope]);
   const agents = useAgentStore((s) => s.agents);
   const agentOrder = useAgentStore((s) => s.agentOrder);
-  const agentVisibility = useUIStore((s) => s.agentVisibility);
   const enabledAgents = useMemo(
     () =>
       sortAgents(
-        agents.filter((a) =>
-          agentVisibility === "detected" ? a.enabled && a.detected : a.enabled,
-        ),
+        agents.filter((a) => a.enabled),
         agentOrder,
       ),
-    [agents, agentOrder, agentVisibility],
+    [agents, agentOrder],
   );
   const resultCount = filtered().length;
 
diff --git a/src/components/extensions/install-dialog.tsx b/src/components/extensions/install-dialog.tsx
index 4147cc6..45b6613 100644
--- a/src/components/extensions/install-dialog.tsx
+++ b/src/components/extensions/install-dialog.tsx
@@ -61,7 +61,7 @@ export function InstallDialog({ open, mode, onClose }: InstallDialogProps) {
   }, [fetchAgents]);
 
   const detectedAgents = sortAgents(
-    agents.filter((a) => a.detected),
+    agents.filter((a) => a.detected && a.enabled),
     agentOrder,
   );
 
diff --git a/src/components/extensions/new-skills-dialog.tsx b/src/components/extensions/new-skills-dialog.tsx
index 3f6a46d..fdc7dd3 100644
--- a/src/components/extensions/new-skills-dialog.tsx
+++ b/src/components/extensions/new-skills-dialog.tsx
@@ -42,7 +42,7 @@ export function NewSkillsDialog({
   const agents = useAgentStore((s) => s.agents);
   const agentOrder = useAgentStore((s) => s.agentOrder);
   const detectedAgents = sortAgents(
-    agents.filter((a) => a.detected),
+    agents.filter((a) => a.detected && a.enabled),
     agentOrder,
   );
 
diff --git a/src/pages/marketplace.tsx b/src/pages/marketplace.tsx
index ac86954..9d97ae3 100644
--- a/src/pages/marketplace.tsx
+++ b/src/pages/marketplace.tsx
@@ -405,7 +405,7 @@ export default function MarketplacePage() {
   };
 
   const detectedAgents = sortAgents(
-    agents.filter((a) => a.detected),
+    agents.filter((a) => a.detected && a.enabled),
     agentOrder,
   );
   const displayItems = query.length >= 2 ? results : trending;
diff --git a/src/pages/overview.tsx b/src/pages/overview.tsx
index a81965b..db5314b 100644
--- a/src/pages/overview.tsx
+++ b/src/pages/overview.tsx
@@ -27,7 +27,6 @@ import { useAgentStore } from "@/stores/agent-store";
 import { useAuditStore } from "@/stores/audit-store";
 import { buildGroups, useExtensionStore } from "@/stores/extension-store";
 import { toast } from "@/stores/toast-store";
-import { useUIStore } from "@/stores/ui-store";
 
 // ---------------------------------------------------------------------------
 // Tip of the Day types & helpers
@@ -200,7 +199,6 @@ export default function OverviewPage() {
   const agents = useAgentStore((s) => s.agents);
   const fetchAgents = useAgentStore((s) => s.fetch);
   const agentOrder = useAgentStore((s) => s.agentOrder);
-  const agentVisibility = useUIStore((s) => s.agentVisibility);
 
   const [agentConfigs, setAgentConfigs] = useState<AgentDetail[]>([]);
   const [auditLoading, setAuditLoading] = useState(false);
@@ -317,18 +315,14 @@ export default function OverviewPage() {
     () =>
       sortAgents(
         agents
-          .filter((a) =>
-            agentVisibility === "detected"
-              ? a.enabled && a.detected
-              : a.enabled,
-          )
+          .filter((a) => a.enabled)
           .map((a) => ({
             ...a,
             extension_count: agentExtCounts.get(a.name) ?? 0,
           })),
         agentOrder,
       ),
-    [agents, agentExtCounts, agentOrder, agentVisibility],
+    [agents, agentExtCounts, agentOrder],
   );
 
   // -----------------------------------------------------------------------