diff --git a/PyTeX/build/build/builder.py b/PyTeX/build/build/builder.py
index def7bad..ed56dc2 100644
--- a/PyTeX/build/build/builder.py
+++ b/PyTeX/build/build/builder.py
@@ -1,5 +1,6 @@
 from pathlib import Path
 from typing import Optional, Union, List, Tuple, Set
+import shutil
 
 from .enums import PyTeXRootDirType
 from .pytex_config import PyTeXConfig
@@ -173,23 +174,24 @@ class PyTeXBuilder:
             raise NotImplementedError  # what to do in this case? dependency does not exist...
 
     def _check_output_directory_integrity(self):
-        out_dir_files = [
+        out_dir_files: List[RelativePath] = [
             RelativePath(self.target_root, file)
             for file in self.target_root.rglob('*')
         ]
         for file in out_dir_files:
-            version = self._old_version_lookup(file)
-            if version.file_hash != md5(file.path):
-                if self.pytex_config.clean_old_files:
-                    raise NotImplementedError  # Not ok
-                else:
-                    if self.pytex_config.overwrite_existing_files:
-                        self._files_to_overwrite.add(file)
+            if not file.relative_path.is_dir():
+                version = self._old_version_lookup(file)
+                if version.file_hash != md5(file.path):
+                    if self.pytex_config.clean_old_files:
+                        raise NotImplementedError  # Not ok
                     else:
-                        if file.relative_path in \
-                                {x.relative_path.relative_path for x in self._files_to_build}:
-                            raise NotImplementedError
-                            # Not ok iff we are going to write this file
+                        if self.pytex_config.overwrite_existing_files:
+                            self._files_to_overwrite.add(file)
+                        else:
+                            if file.relative_path in \
+                                    {x.relative_path.relative_path for x in self._files_to_build}:
+                                raise NotImplementedError
+                                # Not ok iff we are going to write this file
 
     def _dependencies_hash(self, pytex_output_file: PyTeXOutputFile) -> str:
         t = pytex_output_file.dependencies
@@ -222,11 +224,22 @@ class PyTeXBuilder:
 
     def _build_files(self):
         for source_file in self._files_to_build:
-            import os
             out_dir = self._tmp_dir / source_file.file_hash
             out_dir.mkdir(exist_ok=False, parents=True)
             source_file.format(self._tmp_dir / source_file.file_hash)
 
+    def _move_files(self):
+        for source_file in self._files_to_build:
+            tmp_dir = self._tmp_dir / source_file.file_hash
+            for filename in source_file.output_files:
+                out_dir = self.target_root / source_file.relative_path.relative_path.parent
+                out_dir.mkdir(parents=True, exist_ok=True)
+                shutil.move(
+                    tmp_dir / filename.relative_path.name,
+                    out_dir / filename.relative_path.name
+                )
+        shutil.rmtree(self._tmp_dir)
+
     def _build(self) -> bool:
         logger.info("Starting build")
         self._load_pytex_files()
@@ -238,4 +251,5 @@ class PyTeXBuilder:
         self._check_output_directory_integrity()
         logger.info(f"Starting build")
         self._build_files()
+        self._move_files()
         return True
diff --git a/PyTeX/build/build/pytex_file.py b/PyTeX/build/build/pytex_file.py
index c875a39..cb4b756 100644
--- a/PyTeX/build/build/pytex_file.py
+++ b/PyTeX/build/build/pytex_file.py
@@ -53,7 +53,7 @@ class PyTeXSourceFile:
             raise NotImplementedError  # TODO
         files: List[str] = self._formatter.output_files
         paths = [
-            self._relative_path.with_name(filename)
+            RelativePath(self._relative_path.root_dir, self._relative_path.with_name(filename))
             for filename in files
         ]
         return paths