diff --git a/scripts/bootstrap.py b/scripts/bootstrap.py
index 0d20a35..af94155 100644
--- a/scripts/bootstrap.py
+++ b/scripts/bootstrap.py
@@ -876,15 +876,6 @@ def main() -> int:
             if hydrus_script.exists():
                 try:
                     subprocess.check_call([sys.executable, str(hydrus_script)])
-                    
-                    # New: Prompt for location as requested
-                    print("\n" + "="*40)
-                    print("   HYDRUS CONFIGURATION")
-                    print("="*40)
-                    location = input("\nEnter the absolute path to your Hydrus git clone\n(to link it with Medios-Macina config): ").strip()
-                    if location:
-                        if _update_config_value(repo_root, "gitclone", location):
-                            print(f"✅ Updated config.conf with gitclone=\"{location}\"")
                 except subprocess.CalledProcessError:
                     print("\nHydrusNetwork setup exited with an error.")
                 except Exception as e:
diff --git a/scripts/hydrusnetwork.py b/scripts/hydrusnetwork.py
index fc3b5f2..8e58761 100644
--- a/scripts/hydrusnetwork.py
+++ b/scripts/hydrusnetwork.py
@@ -29,6 +29,7 @@ import tempfile
 import urllib.request
 import zipfile
 import shlex
+import re
 from pathlib import Path
 from typing import Optional, Tuple
 
@@ -143,6 +144,45 @@ def run_git_pull(git: str, dest: Path) -> None:
     subprocess.run([git, "-C", str(dest), "pull"], check=True)
 
 
+def update_medios_config(hydrus_path: Path) -> bool:
+    """Attempt to update config.conf in the Medios-Macina root with the hydrus path.
+    
+    This helps link the newly installed Hydrus instance with the main project.
+    """
+    # Scripts is in <root>/scripts, so parent is root.
+    script_dir = Path(__file__).resolve().parent
+    root = script_dir.parent
+    config_path = root / "config.conf"
+    
+    if not config_path.exists():
+        logging.debug("MM config.conf not found at %s; skipping auto-link.", config_path)
+        return False
+        
+    try:
+        content = config_path.read_text(encoding="utf-8")
+        key = "gitclone"
+        value = str(hydrus_path.resolve())
+        
+        # Pattern to replace existing gitclone in the hydrusnetwork section
+        pattern = rf'^(\s*{re.escape(key)}\s*=\s*)(.*)$'
+        if re.search(pattern, content, flags=re.MULTILINE):
+            new_content = re.sub(pattern, rf'\1"{value}"', content, flags=re.MULTILINE)
+        else:
+            section_pattern = r'\[store=hydrusnetwork\]'
+            if re.search(section_pattern, content):
+                new_content = re.sub(section_pattern, f'[store=hydrusnetwork]\n{key}="{value}"', content, count=1)
+            else:
+                new_content = content + f'\n\n[store=hydrusnetwork]\nname="hydrus"\n{key}="{value}"'
+        
+        if new_content != content:
+            config_path.write_text(new_content, encoding="utf-8")
+            logging.info("✅ Linked Hydrus installation in Medios-Macina config (gitclone=\"%s\")", value)
+            return True
+    except Exception as e:
+        logging.debug("Failed to update MM config: %s", e)
+    return False
+
+
 def download_and_extract_zip(
     repo_url: str,
     dest: Path,
@@ -690,12 +730,20 @@ def main(argv: Optional[list[str]] = None) -> int:
         action="store_true",
         help="Perform a full clone (no --depth passed to git clone)"
     )
-    parser.add_argument(
+    group_obtain = parser.add_mutually_exclusive_group()
+    group_obtain.add_argument(
         "--git",
+        dest="git",
         action="store_true",
-        help=
-        "Use git clone instead of fetching repository ZIP (opt-in). Default: fetch ZIP (smaller).",
+        help="Use git clone (shallow by default) to allow updates. This is the default.",
     )
+    group_obtain.add_argument(
+        "--no-git",
+        dest="git",
+        action="store_false",
+        help="Use ZIP download instead of git clone (no git pull support).",
+    )
+    parser.set_defaults(git=True)
     parser.add_argument(
         "--no-fallback",
         action="store_true",
@@ -857,6 +905,7 @@ def main(argv: Optional[list[str]] = None) -> int:
                         try:
                             run_git_pull(git, dest)
                             logging.info("Updated repository in %s", dest)
+                            update_medios_config(dest)
                             return 0
                         except subprocess.CalledProcessError as e:
                             logging.error("git pull failed: %s", e)
@@ -975,14 +1024,14 @@ def main(argv: Optional[list[str]] = None) -> int:
                                     "python-dateutil": "dateutil",
                                     "beautifulsoup4": "bs4",
                                     "pillow-heif": "pillow_heif",
-                                    "pillow-jxl-plugin": "pillow_jxl_plugin",
+                                    "pillow-jxl-plugin": "pillow_jxl",
                                     "pyopenssl": "OpenSSL",
                                     "pysocks": "socks",
                                     "service-identity": "service_identity",
-                                    "show-in-file-manager": "show_in_file_manager",
                                     "opencv-python-headless": "cv2",
-                                    "mpv": "mpv",
-                                    "pyside6": "PySide6",
+                                    "pyyside6": "PySide6",
+                                    "pyside6-essentials": "PySide6",
+                                    "pyside6-addons": "PySide6",
                                 }
                                 for pkg in pkgs:
                                     mod = import_map.get(pkg, pkg)
@@ -1176,6 +1225,10 @@ def main(argv: Optional[list[str]] = None) -> int:
                 logging.error("Failed to obtain repository (ZIP): %s", exc)
                 return 7
 
+        # Auto-link to Medios-Macina if possible
+        if obtained:
+            update_medios_config(dest)
+
         # Post-obtain setup: create repository-local venv (unless disabled)
         if not getattr(args, "no_venv", False):
             try: