config: warn on file-path override across included configs

Replace silent files.extend() with explicit override detection: when a
later-included config redefines a [[files]] path, warn on the console and
replace in place (last definition wins, no duplicate left). Makes the
previously-invisible, order-dependent config override visible.

src/config/mod.rs

@@ -102,7 +102,27 @@ impl Config {
             self.packages.insert(package, package_config);
         }
 
-        self.files.extend(other_files);
+        // File entries from later-included configs override earlier ones for
+        // the same path. Previously this was `self.files.extend(other_files)`,
+        // which silently accumulated duplicate paths and left the winner to
+        // whichever entry the installer wrote last — an invisible, order-
+        // dependent override that is a frequent source of "my config edit did
+        // nothing" confusion (e.g. an init service redefined by a legacy
+        // overlay config). Make the override explicit and visible: warn on the
+        // console and replace in place so the last definition deterministically
+        // wins with no duplicate left in the list.
+        for file in other_files {
+            if let Some(existing) = self.files.iter_mut().find(|f| f.path == file.path) {
+                eprintln!(
+                    "config: WARNING: file '{}' redefined by a later-included config \
+                     (override — last definition wins)",
+                    file.path
+                );
+                *existing = file;
+            } else {
+                self.files.push(file);
+            }
+        }
 
         for (user, user_config) in other_users {
             self.users.insert(user, user_config);