Auto-detect CI/TUI mode for non-interactive environments and improve patch application robustness

- apply-patches.sh: add signature-marker checks for build-system patches
  to handle cases where reverse-check fails but patch is already applied
- test-baremetal.sh: auto-disable TUI when stdout is not a terminal;
  pass CI=1 to make
- test-live-iso-qemu.sh: pass CI=1 via env to prevent repo cook panic
- scripts/run.sh: auto-disable TUI when stdout is not a terminal;
  pass CI=1 to qemu launch
- repo.rs: improve TUI initialization error messages (raw mode + alternate
  screen) and rustfmt cleanups
- config.rs: auto-detect TTY presence for TUI enablement; use is_terminal()
  instead of relying solely on CI env var

src/bin/repo.rs

@@ -1032,7 +1032,11 @@ impl TuiApp {
         thread::spawn(move || {
             while let Ok(msg) = log_writer_rx.recv() {
                 match msg {
-                    LogWriterMessage::Write { _name, path, content } => {
+                    LogWriterMessage::Write {
+                        _name,
+                        path,
+                        content,
+                    } => {
                         if content.trim_end().is_empty() {
                             continue;
                         }
@@ -1157,10 +1161,8 @@ impl TuiApp {
             }
             StatusUpdate::FlushLog(name, path) => {
                 let (logs, line) = self.get_recipe_log(&name);
-                let content = strip_ansi_escapes::strip_str(join_logs(
-                    logs.unwrap_or(&Vec::new()),
-                    line,
-                ));
+                let content =
+                    strip_ansi_escapes::strip_str(join_logs(logs.unwrap_or(&Vec::new()), line));
                 let _ = self.log_writer_tx.send(LogWriterMessage::Write {
                     _name: name,
                     path,
@@ -1328,9 +1330,9 @@ fn run_tui_cook(config: CliConfig, recipes: Vec<CookRecipe>) -> Result<TuiApp, c
     let mstdin = stdin();
     let mstdout = stdout()
         .into_raw_mode()
-        .unwrap()
+        .map_err(|e| Error::from_io_error(e, "Entering raw terminal mode (try CI=1)"))?
         .into_alternate_screen()
-        .unwrap();
+        .map_err(|e| Error::from_io_error(e, "Entering alternate terminal screen"))?;
 
     // ----- Input Thread -----
     let (input_tx, input_rx) = mpsc::channel::<Event>();

src/config.rs

@@ -1,4 +1,10 @@
-use std::{collections::HashMap, env, fs, str::FromStr, sync::OnceLock};
+use std::{
+    collections::HashMap,
+    env, fs,
+    io::{IsTerminal, stdin},
+    str::FromStr,
+    sync::OnceLock,
+};
 
 use serde::{Deserialize, Serialize};
 
@@ -86,7 +92,9 @@ pub fn init_config() {
     };
 
     if config.cook_opt.tui.is_none() {
-        config.cook_opt.tui = Some(!env::var("CI").is_ok_and(|s| !s.is_empty()));
+        let ci_set = env::var("CI").is_ok_and(|s| !s.is_empty());
+        let tty = stdin().is_terminal();
+        config.cook_opt.tui = Some(!ci_set && tty);
     }
     if config.cook_opt.jobs.is_none() {
         config.cook_opt.jobs = Some(extract_env(