fix(check): skip exported config for formatters when workspace file exists

Load repository config files into the staging area before exported
configs so that workspace files take precedence. The existing
to.exists() guard in load_config_file_from naturally skips the
exported config when the workspace file is already present,
making formatter behavior consistent with linters.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: marschattha

qlty-check/src/executor.rs

@@ -314,7 +314,20 @@ impl Executor {
 
         let mut loaded_config_files = vec![];
 
-        // load exported config paths before anything else
+        // load repository config files first so that workspace files take
+        // precedence over exported configs in the staging area
+        for config_file in &repository_config_files {
+            if let Err(err) = load_config_file_from_repository(
+                config_file,
+                &self.plan.workspace,
+                &self.plan.staging_area.destination_directory,
+            ) {
+                error!("Failed to load config file from repository: {:?}", err);
+            }
+        }
+
+        // load exported config paths — these are skipped if the file already
+        // exists in the destination (e.g. from a workspace config file above)
         for config_file in &exported_config_paths {
             if self.plan.workspace.root != self.plan.staging_area.destination_directory {
                 // for formatters
@@ -337,16 +350,6 @@ impl Executor {
         self.check_and_copy_configs_into_tool_install(&mut loaded_config_files)?;
         self.plan_plugins_fetch(&mut loaded_config_files)?;
 
-        for config_file in &repository_config_files {
-            if let Err(err) = load_config_file_from_repository(
-                config_file,
-                &self.plan.workspace,
-                &self.plan.staging_area.destination_directory,
-            ) {
-                error!("Failed to load config file from repository: {:?}", err);
-            }
-        }
-
         for config_file in &config_file_names {
             if self.plan.workspace.root != self.plan.staging_area.destination_directory {
                 // for formatters