fix: link residuetypedat (#488)

* fix: link residuetypedat
* create symlink by default without config option

src/kimmdy/runmanager.py

@@ -249,7 +249,8 @@ def run(self):
         logger.info("Start run")
         self.start_time = time.time()
 
-        if getattr(self.config.restart, "run_directory", None):
+        if restart_dir := getattr(self.config.restart, "run_directory", None):
+            logger.info(f"Restarting from: {restart_dir}")
             self._restart_from_rundir()
 
         while (
@@ -447,7 +448,9 @@ def _setup(self, files: TaskFiles) -> TaskFiles:
             if hasattr(self.config, f):
                 if path := self.latest_files.get(f):
                     logger.debug(f"Copying {path} to {files.outputdir}")
-                    shutil.copy(path, files.outputdir / path.name)
+                    shutil.copy(
+                        path, files.outputdir / path.name, follow_symlinks=False
+                    )
                     files.output[f] = files.outputdir / path.name
 
         return files

src/kimmdy/tasks.py

@@ -106,6 +106,10 @@ def create_task_directory(runmng, postfix: str) -> TaskFiles:
     if runmng.config.ff is not None:
         if not (files.outputdir / runmng.config.ff.name).exists():
             (files.outputdir / runmng.config.ff.name).symlink_to(runmng.config.ff)
+        if not (files.outputdir / "residuetypes.dat").exists():
+            (files.outputdir / "residuetypes.dat").symlink_to(
+                runmng.config.ff / "residuetypes.dat"
+            )
 
     return files