diff --git a/bin/dev/check-boundary.sh b/bin/dev/check-boundary.sh
index 7771d58ed..974dc4442 100755
--- a/bin/dev/check-boundary.sh
+++ b/bin/dev/check-boundary.sh
@@ -3,8 +3,14 @@ set -euo pipefail
 
 cd "$(dirname "$0")/../.."
 
-symbol_allowlist=(
+server_symbol_allowlist=(
   "lib/crates/fabro-cli/src/local_server.rs"
+  "lib/crates/fabro-cli/src/commands/run/runner.rs"
+  "lib/crates/fabro-cli/src/commands/pr/mod.rs"
+  "lib/crates/fabro-cli/src/commands/pr/create.rs"
+)
+
+storage_allowlist=(
   "lib/crates/fabro-cli/src/commands/install.rs"
   "lib/crates/fabro-cli/src/commands/uninstall.rs"
   "lib/crates/fabro-cli/src/commands/run/runner.rs"
@@ -50,11 +56,19 @@ fail=0
 
 while IFS= read -r path; do
   [[ -z "$path" ]] && continue
-  if ! in_array "$path" "${symbol_allowlist[@]}"; then
+  if ! in_array "$path" "${server_symbol_allowlist[@]}"; then
     echo "boundary check failed: gated server symbol used outside allowlist: $path" >&2
     fail=1
   fi
-done < <(find_matches 'fabro_config::resolve_server_from_file|fabro_config::resolve_server\b|fabro_config::ServerSettings::from_layer\b|fabro_config::ServerSettings::resolve\b|ServerSettings::from_layer\b|ServerSettings::resolve\b|Storage::new')
+done < <(find_matches 'fabro_config::resolve_server_from_file|fabro_config::resolve_server\b|fabro_config::ServerSettings::from_layer\b|fabro_config::ServerSettings::resolve\b|ServerSettings::from_layer\b|ServerSettings::resolve\b')
+
+while IFS= read -r path; do
+  [[ -z "$path" ]] && continue
+  if ! in_array "$path" "${storage_allowlist[@]}"; then
+    echo "boundary check failed: Storage::new used outside allowlist: $path" >&2
+    fail=1
+  fi
+done < <(find_matches 'Storage::new')
 
 while IFS= read -r path; do
   [[ -z "$path" ]] && continue
diff --git a/lib/crates/fabro-cli/src/commands/install.rs b/lib/crates/fabro-cli/src/commands/install.rs
index 886524266..fa9d26f73 100644
--- a/lib/crates/fabro-cli/src/commands/install.rs
+++ b/lib/crates/fabro-cli/src/commands/install.rs
@@ -1277,8 +1277,7 @@ async fn write_artifact_store_metadata(
     settings: &SettingsLayer,
     fabro_version: &str,
 ) -> Result<()> {
-    let resolved =
-        fabro_config::ServerSettings::from_layer(settings).map_err(anyhow::Error::from)?;
+    let resolved = local_server::server_settings(settings)?;
     let (object_store, prefix) = serve::build_artifact_object_store(&resolved.server)?;
     let artifact_store = ArtifactStore::new(object_store, prefix);
     artifact_store.write_metadata(fabro_version).await?;
@@ -1797,7 +1796,7 @@ async fn run_install_inner(
             .context("failed to parse generated settings.toml")?,
         args.storage_dir.as_deref(),
     );
-    fabro_config::ServerSettings::from_layer(&install_settings).map_err(anyhow::Error::from)?;
+    local_server::server_settings(&install_settings)?;
 
     // Secrets and auth material
     {
diff --git a/lib/crates/fabro-cli/src/local_server.rs b/lib/crates/fabro-cli/src/local_server.rs
index cdba3b556..5128e70da 100644
--- a/lib/crates/fabro-cli/src/local_server.rs
+++ b/lib/crates/fabro-cli/src/local_server.rs
@@ -26,8 +26,12 @@ pub(crate) fn bind_request(
     resolve_bind_request_from_settings(settings, cli_override)
 }
 
+pub(crate) fn server_settings(settings: &SettingsLayer) -> Result<fabro_config::ServerSettings> {
+    fabro_config::ServerSettings::from_layer(settings).map_err(anyhow::Error::from)
+}
+
 pub(crate) fn auth_methods(settings: &SettingsLayer) -> Vec<ServerAuthMethod> {
-    fabro_config::ServerSettings::from_layer(settings)
+    server_settings(settings)
         .map(|resolved| resolved.server.auth.methods)
         .unwrap_or_default()
 }
diff --git a/lib/crates/fabro-cli/tests/it/scenario/smoke.rs b/lib/crates/fabro-cli/tests/it/scenario/smoke.rs
index 13160b955..cf1db65fb 100644
--- a/lib/crates/fabro-cli/tests/it/scenario/smoke.rs
+++ b/lib/crates/fabro-cli/tests/it/scenario/smoke.rs
@@ -134,16 +134,12 @@ fn help_smoke_covers_high_cost_commands() {
     ----- stdout -----
     Inspect effective settings
 
-    Usage: fabro settings [OPTIONS] [WORKFLOW]
-
-    Arguments:
-      [WORKFLOW]  Optional workflow name, .fabro path, or .toml run config to overlay
+    Usage: fabro settings [OPTIONS]
 
     Options:
           --json              Output as JSON [env: FABRO_JSON=]
           --server <SERVER>   Fabro server target: http(s) URL or absolute Unix socket path [env: FABRO_SERVER=]
           --debug             Enable DEBUG-level logging (default is INFO) [env: FABRO_DEBUG=]
-          --local             Show only locally resolved settings and skip the server call
           --no-upgrade-check  Disable automatic upgrade check [env: FABRO_NO_UPGRADE_CHECK=true]
           --quiet             Suppress non-essential output [env: FABRO_QUIET=]
           --verbose           Enable verbose output [env: FABRO_VERBOSE=]
diff --git a/lib/crates/fabro-server/src/serve.rs b/lib/crates/fabro-server/src/serve.rs
index 49ae4d959..0055eb108 100644
--- a/lib/crates/fabro-server/src/serve.rs
+++ b/lib/crates/fabro-server/src/serve.rs
@@ -901,6 +901,7 @@ mod tests {
         resolve_server_settings, resolve_startup_github_webhook_ip_allowlist, router_web_enabled,
         server_bind_title, server_title,
     };
+    use crate::server::create_app_state_with_options;
 
     fn parse_settings(source: &str) -> SettingsLayer {
         let mut layer = parse_settings_layer(source).expect("v2 fixture should parse");
@@ -935,6 +936,42 @@ mod tests {
         assert_eq!(storage_root.as_deref(), Some("/srv/fabro-storage"));
     }
 
+    #[test]
+    fn app_state_server_settings_use_effective_runtime_layer_storage_override() {
+        let base = parse_settings(
+            r#"
+_version = 1
+
+[server.storage]
+root = "/srv/from-disk"
+"#,
+        );
+        let args = ServeArgs {
+            bind: None,
+            model: None,
+            provider: None,
+            sandbox: None,
+            web: false,
+            no_web: false,
+            max_concurrent_runs: None,
+            config: None,
+            #[cfg(debug_assertions)]
+            watch_web: false,
+        };
+
+        let effective = apply_runtime_settings(&base, &args, &PathBuf::from("/srv/from-runtime"));
+        let state = create_app_state_with_options(effective, 5);
+
+        assert_eq!(
+            state.server_settings().server.storage.root.as_source(),
+            "/srv/from-runtime"
+        );
+        assert_eq!(
+            state.server_storage_dir(),
+            PathBuf::from("/srv/from-runtime")
+        );
+    }
+
     #[test]
     fn apply_runtime_settings_enables_web_from_cli_flag() {
         let base = parse_settings(
diff --git a/lib/crates/fabro-server/src/server.rs b/lib/crates/fabro-server/src/server.rs
index fa97ac90e..6d2526cb1 100644
--- a/lib/crates/fabro-server/src/server.rs
+++ b/lib/crates/fabro-server/src/server.rs
@@ -7397,6 +7397,65 @@ url = "{url}"
         }
     }
 
+    #[test]
+    fn replace_settings_updates_layer_and_typed_server_settings() {
+        let state = create_app_state_with_options(
+            fabro_config::parse_settings_layer(
+                r#"
+_version = 1
+
+[server.auth]
+methods = ["dev-token"]
+
+[server.web]
+url = "http://old.example.com"
+
+[server.storage]
+root = "/srv/old"
+"#,
+            )
+            .expect("settings fixture should parse"),
+            5,
+        );
+
+        let updated = fabro_config::parse_settings_layer(
+            r#"
+_version = 1
+
+[server.auth]
+methods = ["dev-token"]
+
+[server.web]
+url = "http://new.example.com"
+
+[server.storage]
+root = "/srv/new"
+"#,
+        )
+        .expect("settings fixture should parse");
+
+        state
+            .replace_settings(updated)
+            .expect("valid settings should replace current state");
+
+        assert_eq!(state.canonical_origin().unwrap(), "http://new.example.com");
+        assert_eq!(
+            state.server_settings().server.storage.root.as_source(),
+            "/srv/new"
+        );
+
+        let layer_root = state
+            .settings
+            .read()
+            .expect("settings lock poisoned")
+            .server
+            .as_ref()
+            .and_then(|server| server.storage.as_ref())
+            .and_then(|storage| storage.root.as_ref())
+            .map(InterpString::as_source);
+        assert_eq!(layer_root.as_deref(), Some("/srv/new"));
+    }
+
     #[tokio::test]
     async fn create_secret_stores_file_secret_and_excludes_it_from_snapshot() {
         let state = create_app_state();