diff --git a/.gitignore b/.gitignore
index 4465530..c43da6a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,16 +2,17 @@
 .idea/
 .vscode/
 
-# Runtime config
-config.yaml
-config.yaml.*
+# Local env
+.env
 
-# Build / runtime artifacts
-resources/dist/
-resources/zip/*
+# Runtime
+runtime/
 
-# 保留 dist.zip
-!resources/zip/dist.zip
+# Local dashboard unpacked files
+resources/dashboard/dist/
 
-# 临时脚本
+# Keep packaged dashboard asset
+!resources/dashboard/dist.zip
+
+# Local test scripts
 test.sh
diff --git a/README.md b/README.md
index 9e895eb..ce8bde6 100644
--- a/README.md
+++ b/README.md
@@ -197,6 +197,7 @@ Control 层负责把常用动作收口成可理解的命令和反馈。
 - `runtime/` 是唯一运行时容器
 - 后端可以是 `systemd`、`systemd-user` 或 `script`
 - 运行配置是 `runtime/config.yaml`
+- 订阅集合状态是 `runtime/subscriptions.yaml`（历史 `config/subscriptions.yaml` 仅用于兼容迁移）
 - 日志、状态、缓存和运行时产物都收敛到 runtime 体系
 
 ## 配置说明
diff --git a/config/subscriptions.yaml b/config/subscriptions.yaml
deleted file mode 100644
index 847c8c9..0000000
--- a/config/subscriptions.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-active: default
-
-sources:
-  default:
-    type: clash
-    url: ""
-    enabled: true
diff --git a/scripts/core/config.sh b/scripts/core/config.sh
index b27279c..0a9827b 100644
--- a/scripts/core/config.sh
+++ b/scripts/core/config.sh
@@ -57,7 +57,7 @@ clear_build_error_detail() {
 }
 
 subscriptions_file() {
-  echo "$CONFIG_DIR/subscriptions.yaml"
+  echo "$RUNTIME_DIR/subscriptions.yaml"
 }
 
 migrate_subscriptions_legacy_fields() {
@@ -81,15 +81,25 @@ migrate_subscriptions_legacy_fields() {
 }
 
 ensure_subscriptions_file() {
-  local file
+  local file legacy_file
   file="$(subscriptions_file)"
+  legacy_file="$CONFIG_DIR/subscriptions.yaml"
 
   if [ -f "$file" ]; then
     migrate_subscriptions_legacy_fields "$file"
     return 0
   fi
 
-  mkdir -p "$CONFIG_DIR"
+  mkdir -p "$RUNTIME_DIR"
+
+  if [ -f "$legacy_file" ]; then
+    mv -f "$legacy_file" "$file" 2>/dev/null || {
+      cp -f "$legacy_file" "$file"
+      rm -f "$legacy_file" 2>/dev/null || true
+    }
+    migrate_subscriptions_legacy_fields "$file"
+    return 0
+  fi
 
   cat > "$file" <<'EOF'
 active: default
diff --git a/scripts/core/update.sh b/scripts/core/update.sh
index d3a2999..bc4b059 100644
--- a/scripts/core/update.sh
+++ b/scripts/core/update.sh
@@ -34,6 +34,37 @@ git_has_local_changes() {
   [ -n "$(git -C "$PROJECT_DIR" status --porcelain --untracked-files=no 2>/dev/null)" ]
 }
 
+git_has_changes_except_legacy_subscriptions() {
+  git -C "$PROJECT_DIR" status --porcelain --untracked-files=no 2>/dev/null \
+    | awk '{
+        path=substr($0,4)
+        if (path != "config/subscriptions.yaml") {
+          found=1
+        }
+      }
+      END { exit(found?0:1) }'
+}
+
+handle_legacy_subscriptions_dirty_for_update() {
+  local legacy_file runtime_file
+  legacy_file="$CONFIG_DIR/subscriptions.yaml"
+  runtime_file="$(subscriptions_file)"
+
+  git_has_local_changes || return 1
+  git_has_changes_except_legacy_subscriptions && return 1
+
+  info "检测到历史路径 config/subscriptions.yaml 的本地改动，正在执行迁移兜底"
+
+  if [ -f "$legacy_file" ] && [ ! -f "$runtime_file" ]; then
+    mkdir -p "$RUNTIME_DIR"
+    cp -f "$legacy_file" "$runtime_file" 2>/dev/null || true
+    migrate_subscriptions_legacy_fields "$runtime_file"
+  fi
+
+  git -C "$PROJECT_DIR" checkout -- config/subscriptions.yaml >/dev/null 2>&1 || true
+  return 0
+}
+
 git_remote_name() {
   echo "${CLASH_GIT_REMOTE:-origin}"
 }
@@ -167,6 +198,10 @@ update_project_code() {
   info "远程仓库：$remote_name"
   info "更新分支：$branch"
 
+  if [ "$force_mode" != "true" ]; then
+    handle_legacy_subscriptions_dirty_for_update || true
+  fi
+
   if git_has_local_changes && [ "$force_mode" != "true" ]; then
     die "检测到本地有未提交改动，请先提交，或使用 clashctl update --force"
   fi
diff --git a/uninstall.sh b/uninstall.sh
index 6310d60..3caa3d3 100755
--- a/uninstall.sh
+++ b/uninstall.sh
@@ -60,8 +60,8 @@ elif [ "$DEV_RESET" = "true" ]; then
     cache_restore_needed="true"
   fi
 
-  if [ -f "$CONFIG_DIR/subscriptions.yaml" ]; then
-    cp -f "$CONFIG_DIR/subscriptions.yaml" "$subscriptions_backup_file" 2>/dev/null || true
+  if [ -f "$RUNTIME_DIR/subscriptions.yaml" ]; then
+    cp -f "$RUNTIME_DIR/subscriptions.yaml" "$subscriptions_backup_file" 2>/dev/null || true
     subscriptions_restore_needed="true"
   fi
 
@@ -74,8 +74,8 @@ elif [ "$DEV_RESET" = "true" ]; then
   fi
 
   if [ "$subscriptions_restore_needed" = "true" ] && [ -f "$subscriptions_backup_file" ]; then
-    mkdir -p "$CONFIG_DIR"
-    cp -f "$subscriptions_backup_file" "$CONFIG_DIR/subscriptions.yaml"
+    mkdir -p "$RUNTIME_DIR"
+    cp -f "$subscriptions_backup_file" "$RUNTIME_DIR/subscriptions.yaml"
   fi
 
   rm -rf "$cache_backup_dir" 2>/dev/null || true