diff --git a/src/auth.rs b/src/auth.rs
index 51291a88..935fea4c 100644
--- a/src/auth.rs
+++ b/src/auth.rs
@@ -146,6 +146,10 @@ pub fn resolve_name(agent: &str, name: &str) -> String {
 }
 
 pub fn activate(agent: &str, profile: &str, json: bool) {
+    activate_with(agent, profile, false, json)
+}
+
+pub fn activate_with(agent: &str, profile: &str, reload_daemon: bool, json: bool) {
     let profile = resolve_name(agent, profile);
     if let Err(e) = validate_name(agent, "agent").and_then(|_| validate_name(&profile, "profile")) {
         fail(&e, "", json);
@@ -211,6 +215,19 @@ pub fn activate(agent: &str, profile: &str, json: bool) {
     } else {
         println!("activated {agent}/{profile} — restored {restored} file(s)");
     }
+
+    // Daemon check
+    if crate::auth_runner::daemon_running(agent) {
+        if reload_daemon {
+            if let Err(e) = crate::auth_runner::reload_daemon(agent) {
+                eprintln!("warning: failed to reload daemon: {e}");
+            } else if !json {
+                println!("daemon restarted — auth changes now active");
+            }
+        } else if !json {
+            eprintln!("warning: {agent} daemon is running — auth changes won't take effect until restart. Use --reload-daemon to auto-restart.");
+        }
+    }
 }
 
 pub fn status(agent: Option<&str>, json: bool) {
@@ -722,6 +739,10 @@ fn isolates_dir() -> PathBuf {
 }
 
 pub fn isolate_add(agent: &str, profile: &str, json: bool) {
+    isolate_add_with(agent, profile, false, json)
+}
+
+pub fn isolate_add_with(agent: &str, profile: &str, shallow: bool, json: bool) {
     let dir = isolates_dir().join(agent).join(profile);
     if dir.exists() {
         if json {
@@ -733,17 +754,32 @@ pub fn isolate_add(agent: &str, profile: &str, json: bool) {
     }
     fs::create_dir_all(&dir).expect("create isolate dir");
 
-    // Symlink shared host files
-    for host_file in &[".ssh", ".gitconfig", ".git-credentials"] {
-        let src = home().join(host_file);
-        if src.exists() {
-            symlink_or_copy(&src, &dir.join(host_file));
+    if shallow {
+        // Symlink all host dirs, only auth files are real
+        let host_home = home();
+        for entry in &[".cache", ".config", ".local", "Documents", "Downloads"] {
+            let src = host_home.join(entry);
+            if src.exists() {
+                symlink_or_copy(&src, &dir.join(entry));
+            }
+        }
+    } else {
+        // Symlink shared host files only
+        for host_file in &[".ssh", ".gitconfig", ".git-credentials"] {
+            let src = home().join(host_file);
+            if src.exists() {
+                symlink_or_copy(&src, &dir.join(host_file));
+            }
         }
     }
 
     // Copy auth files from vault profile
     activate_into(agent, profile, &dir);
 
+    // Store metadata
+    let meta = serde_json::json!({"mode": if shallow { "shallow" } else { "deep" }, "agent": agent, "profile": profile});
+    fs::write(dir.join("isolate.json"), serde_json::to_string_pretty(&meta).unwrap() + "\n").ok();
+
     if json {
         println!("{}", serde_json::json!({"agent": agent, "profile": profile, "isolate_dir": dir.to_string_lossy()}));
     } else {
@@ -776,10 +812,12 @@ pub fn isolate_ls(agent: Option<&str>, json: bool) {
             for entry in entries.flatten() {
                 if entry.file_type().map(|t| t.is_dir()).unwrap_or(false) {
                     let p = entry.file_name().to_string_lossy().to_string();
+                    let mode = read_isolate_mode(&agent_dir.join(&p));
                     if json {
-                        results.push(serde_json::json!({"agent": a, "profile": p}));
+                        results.push(serde_json::json!({"agent": a, "profile": p, "mode": mode}));
                     } else {
-                        println!("{a}/{p}");
+                        let mode_str = mode.map_or(String::new(), |m| format!(" ({m})"));
+                        println!("{a}/{p}{mode_str}");
                     }
                 }
             }
@@ -907,6 +945,16 @@ pub fn auth_login(agent: &str, profile: &str, args: &[String], json: bool) {
 }
 
 
+fn read_isolate_mode(dir: &std::path::Path) -> Option<String> {
+    let meta_path = dir.join("isolate.json");
+    if let Ok(data) = fs::read_to_string(&meta_path) {
+        if let Ok(meta) = serde_json::from_str::<serde_json::Value>(&data) {
+            return meta["mode"].as_str().map(|s| s.to_string());
+        }
+    }
+    None
+}
+
 fn activate_into(agent: &str, profile: &str, target_dir: &std::path::Path) {
     let cat = match catalog_for(agent) { Some(c) => c, None => { return; } };
     let vault = profile_dir(agent, profile);
diff --git a/src/main.rs b/src/main.rs
index 8c97d44c..48ebd3ec 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -207,6 +207,9 @@ enum AuthAction {
         profile: String,
         #[arg(long)]
         json: bool,
+        /// Restart agent daemon after auth restore (picks up new auth).
+        #[arg(long)]
+        reload_daemon: bool,
     },
     /// Show active profile via content-hash detection.
     Status {
@@ -327,6 +330,9 @@ enum IsolateAction {
         profile: String,
         #[arg(long)]
         json: bool,
+        /// Shallow mode: only auth files copied, everything else symlinked from host.
+        #[arg(long)]
+        shallow: bool,
     },
     /// List isolated profiles.
     Ls {
@@ -439,7 +445,7 @@ fn main() {
         },
         Commands::Auth { action } => match action {
             AuthAction::Backup { agent, profile, json } => auth::backup(&agent, &profile, json),
-            AuthAction::Activate { agent, profile, json } => auth::activate(&agent, &profile, json),
+            AuthAction::Activate { agent, profile, json, reload_daemon } => auth::activate_with(&agent, &profile, reload_daemon, json),
             AuthAction::Status { agent, json } => auth::status(agent.as_deref(), json),
             AuthAction::Catalog { json } => auth::list_agents(json),
             AuthAction::Ls { agent, json } => auth::ls(&agent, json),
@@ -461,7 +467,7 @@ fn main() {
             },
             AuthAction::Run { agent, json, args } => auth_runner::run(&agent, &args, json),
             AuthAction::Isolate { action } => match action {
-                IsolateAction::Add { agent, profile, json } => auth::isolate_add(&agent, &profile, json),
+                IsolateAction::Add { agent, profile, json, shallow } => auth::isolate_add_with(&agent, &profile, shallow, json),
                 IsolateAction::Ls { agent, json } => auth::isolate_ls(agent.as_deref(), json),
                 IsolateAction::Delete { agent, profile, json } => auth::isolate_delete(&agent, &profile, json),
             },