- Move .data into tests/.data, clarifying its usage

-- Update logic and tests to handle this directory
-- Update gitignore to stop tracking temporary folders (`tests/.data` and `.pipelines/*/`)

Changes to be committed:
	deleted:    .data/ztbeMA28ILtxhTRp_mnCXhJYSARd/fc2yNy-pQG2J5fqcRs99tA/generate_c11_c12_dataset/run_calculations/6245/input.gjf
	deleted:    .data/ztbeMA28ILtxhTRp_mnCXhJYSARd/fc2yNy-pQG2J5fqcRs99tA/generate_c11_c12_dataset/run_calculations/6245/input_smiles.txt
	deleted:    .data/ztbeMA28ILtxhTRp_mnCXhJYSARd/fc2yNy-pQG2J5fqcRs99tA/generate_c11_c12_dataset/run_calculations/6245/molecule.mol
	deleted:    .data/ztbeMA28ILtxhTRp_mnCXhJYSARd/manifest.json
	modified:   .gitignore
	modified:   src/parse_patrol/databases/nomad/utils.py
	modified:   tests/example_integration_test.py
	modified:   tests/test_nomad_integration.py

Author: ndaelman-hu

.data/ztbeMA28ILtxhTRp_mnCXhJYSARd/fc2yNy-pQG2J5fqcRs99tA/generate_c11_c12_dataset/run_calculations/6245/input.gjf

@@ -1,5 +1,8 @@
-# Repo
-.data
+# Project folders
+.pipelines/data
+.pipelines/resources
+.pipelines/scripts
+tests/.data
 
 # VS Code
 .vscode/

.data/ztbeMA28ILtxhTRp_mnCXhJYSARd/fc2yNy-pQG2J5fqcRs99tA/generate_c11_c12_dataset/run_calculations/6245/input_smiles.txt

@@ -178,17 +178,18 @@ def nomad_search_entries(
         raise Exception(f"Failed to query NOMAD API: {str(e)}")
 
 
-def nomad_get_raw_files(entry_id: str) -> str:
-    """Download and extract NOMAD raw files to .data directory.
+def nomad_get_raw_files(entry_id: str, data_root: str='tests/.data') -> str:
+    """Download and extract NOMAD raw files.
 
     Args:
         entry_id: NOMAD entry ID
+        data_root: Optional root directory for downloads. Defaults to tests/.data if not specified.
 
     Returns:
         Path to extracted files directory
     """
     # Create entry-specific directory
-    data_dir = Path(".data") / entry_id
+    data_dir = Path(data_root) / entry_id
     data_dir.mkdir(parents=True, exist_ok=True)
 
     # Check if files already downloaded

.data/ztbeMA28ILtxhTRp_mnCXhJYSARd/fc2yNy-pQG2J5fqcRs99tA/generate_c11_c12_dataset/run_calculations/6245/molecule.mol

@@ -144,7 +144,7 @@ def test_simple_download_and_parse():
         # Clean up
         try:
             import shutil
-            data_dir = Path(".data")
+            data_dir = Path("tests/.data")
             if data_dir.exists():
                 shutil.rmtree(data_dir)
                 print("   🧹 Cleaned up downloaded files")

.data/ztbeMA28ILtxhTRp_mnCXhJYSARd/manifest.json

@@ -90,7 +90,7 @@ def cleanup(self):
                 shutil.rmtree(self.temp_dir)
 
             # Also clean up .data directory entries we created
-            data_dir = Path(".data")
+            data_dir = Path("tests/.data")
             if data_dir.exists():
                 for entry_id in self.downloaded_entries:
                     entry_path = data_dir / entry_id