diff --git a/HIDDEN_FILES_GUIDE.md b/HIDDEN_FILES_GUIDE.md
new file mode 100644
index 0000000..d0259c1
--- /dev/null
+++ b/HIDDEN_FILES_GUIDE.md
@@ -0,0 +1,154 @@
+# Guide de configuration des fichiers et dossiers cachés
+
+## Vue d'ensemble
+
+ObsiGate prend désormais en charge les fichiers et dossiers cachés (ceux qui commencent par un point, comme `.obsidian`, `.git`, etc.) avec une configuration flexible par vault.
+
+## Fonctionnalités
+
+### 1. **Activation globale par vault**
+Vous pouvez activer l'indexation de TOUS les fichiers cachés pour un vault spécifique.
+
+### 2. **Liste blanche flexible**
+Ajoutez des dossiers cachés individuels à une liste blanche, même si l'activation globale est désactivée.
+
+### 3. **Configuration persistante**
+Les paramètres sont sauvegardés et persistent entre les redémarrages.
+
+## Configuration
+
+### Via variables d'environnement
+
+Ajoutez ces variables à votre configuration Docker ou `.env` :
+
+```bash
+# Pour activer tous les fichiers cachés dans un vault
+VAULT_1_INCLUDE_HIDDEN=true
+
+# Pour ajouter des dossiers spécifiques à la liste blanche
+VAULT_1_HIDDEN_WHITELIST=.obsidian,.github,.vscode
+
+# Exemple pour un deuxième vault
+VAULT_2_INCLUDE_HIDDEN=false
+VAULT_2_HIDDEN_WHITELIST=.obsidian
+```
+
+### Via l'interface web
+
+1. Ouvrez le menu **Options** (icône d'engrenage)
+2. Cliquez sur **Configurations**
+3. Faites défiler jusqu'à la section **📁 Fichiers et dossiers cachés**
+4. Pour chaque vault, vous pouvez :
+   - **Activer/désactiver** l'inclusion de tous les fichiers cachés
+   - **Ajouter des dossiers** à la liste blanche individuellement
+   - **Supprimer des dossiers** de la liste blanche
+
+5. Cliquez sur **Sauvegarder les paramètres**
+6. Cliquez sur **Réindexer avec nouveaux paramètres** pour appliquer les changements
+
+## Exemples d'utilisation
+
+### Cas 1 : Indexer uniquement le dossier .obsidian
+
+```bash
+VAULT_1_INCLUDE_HIDDEN=false
+VAULT_1_HIDDEN_WHITELIST=.obsidian
+```
+
+Ou via l'interface :
+- Désactiver "Inclure tous les fichiers cachés"
+- Ajouter `.obsidian` à la liste blanche
+
+### Cas 2 : Indexer tous les fichiers cachés
+
+```bash
+VAULT_1_INCLUDE_HIDDEN=true
+```
+
+Ou via l'interface :
+- Activer "Inclure tous les fichiers cachés"
+
+### Cas 3 : Indexer plusieurs dossiers cachés spécifiques
+
+```bash
+VAULT_1_INCLUDE_HIDDEN=false
+VAULT_1_HIDDEN_WHITELIST=.obsidian,.github,.vscode
+```
+
+Ou via l'interface :
+- Désactiver "Inclure tous les fichiers cachés"
+- Ajouter `.obsidian`, `.github`, `.vscode` à la liste blanche
+
+## API Endpoints
+
+### Obtenir les paramètres d'un vault
+
+```http
+GET /api/vaults/{vault_name}/settings
+```
+
+Réponse :
+```json
+{
+  "includeHidden": false,
+  "hiddenWhitelist": [".obsidian", ".github"]
+}
+```
+
+### Mettre à jour les paramètres d'un vault
+
+```http
+POST /api/vaults/{vault_name}/settings
+Content-Type: application/json
+
+{
+  "includeHidden": true,
+  "hiddenWhitelist": [".obsidian"]
+}
+```
+
+### Obtenir les paramètres de tous les vaults
+
+```http
+GET /api/vaults/settings/all
+```
+
+## Architecture technique
+
+### Backend
+
+- **`backend/indexer.py`** : Fonction `_should_include_path()` qui vérifie si un chemin doit être inclus
+- **`backend/vault_settings.py`** : Gestion de la persistance des paramètres
+- **`backend/main.py`** : Endpoints API pour gérer les paramètres
+- **`backend/attachment_indexer.py`** : Respect des paramètres pour les pièces jointes
+
+### Frontend
+
+- **`frontend/index.html`** : Section de configuration dans le modal
+- **`frontend/app.js`** : Fonctions `loadHiddenFilesSettings()`, `saveHiddenFilesSettings()`, etc.
+- **`frontend/style.css`** : Styles pour l'interface de configuration
+
+## Notes importantes
+
+1. **Réindexation requise** : Après modification des paramètres, une réindexation est nécessaire pour appliquer les changements
+2. **Persistance** : Les paramètres sont sauvegardés dans `/app/data/vault_settings.json`
+3. **Priorité** : Les variables d'environnement sont chargées au démarrage, mais peuvent être écrasées via l'interface web
+4. **Performance** : L'activation de tous les fichiers cachés peut augmenter le temps d'indexation selon le nombre de fichiers
+
+## Dépannage
+
+### Les fichiers cachés n'apparaissent pas après activation
+
+1. Vérifiez que les paramètres sont bien sauvegardés
+2. Déclenchez une réindexation manuelle
+3. Vérifiez les logs du serveur pour d'éventuelles erreurs
+
+### Les paramètres ne persistent pas
+
+1. Vérifiez que le dossier `/app/data/` est accessible en écriture
+2. Vérifiez les permissions du fichier `vault_settings.json`
+3. Consultez les logs pour les erreurs de sauvegarde
+
+### Conflit entre variables d'environnement et interface web
+
+Les paramètres de l'interface web écrasent les variables d'environnement. Pour revenir aux variables d'environnement, supprimez le fichier `vault_settings.json` et redémarrez.
diff --git a/backend/attachment_indexer.py b/backend/attachment_indexer.py
index 86bf411..2d36d20 100644
--- a/backend/attachment_indexer.py
+++ b/backend/attachment_indexer.py
@@ -1,8 +1,10 @@
 import asyncio
 import logging
-import threading
 from pathlib import Path
 from typing import Dict, List, Optional, Set
+import threading
+
+from backend.indexer import _should_include_path
 
 logger = logging.getLogger("obsigate.attachment_indexer")
 
@@ -34,7 +36,7 @@ def clear_resolution_cache(vault_name: Optional[str] = None) -> None:
                 del _resolution_cache[key]
 
 
-def _scan_vault_attachments(vault_name: str, vault_path: str) -> Dict[str, List[Path]]:
+def _scan_vault_attachments(vault_name: str, vault_path: str, vault_cfg: dict = None) -> Dict[str, List[Path]]:
     """Synchronously scan a vault directory for image attachments.
     
     Walks the vault tree and builds a filename -> absolute path mapping
@@ -43,6 +45,7 @@ def _scan_vault_attachments(vault_name: str, vault_path: str) -> Dict[str, List[
     Args:
         vault_name: Display name of the vault.
         vault_path: Absolute filesystem path to the vault root.
+        vault_cfg: Optional vault configuration dict with hidden files settings.
         
     Returns:
         Dict mapping lowercase filenames to lists of absolute paths.
@@ -50,6 +53,10 @@ def _scan_vault_attachments(vault_name: str, vault_path: str) -> Dict[str, List[
     vault_root = Path(vault_path)
     index: Dict[str, List[Path]] = {}
     
+    # Default config if not provided
+    if vault_cfg is None:
+        vault_cfg = {"includeHidden": False, "hiddenWhitelist": []}
+    
     if not vault_root.exists():
         logger.warning(f"Vault path does not exist for attachment scan: {vault_path}")
         return index
@@ -58,9 +65,9 @@ def _scan_vault_attachments(vault_name: str, vault_path: str) -> Dict[str, List[
     
     try:
         for fpath in vault_root.rglob("*"):
-            # Skip hidden files and directories
+            # Check if path should be included based on hidden files configuration
             rel_parts = fpath.relative_to(vault_root).parts
-            if any(part.startswith(".") for part in rel_parts):
+            if not _should_include_path(rel_parts, vault_cfg):
                 continue
             
             # Only process files
@@ -121,7 +128,7 @@ async def build_attachment_index(vault_config: Dict[str, Dict[str, any]]) -> Non
             new_index[name] = {}
             continue
         
-        tasks.append((name, loop.run_in_executor(None, _scan_vault_attachments, name, vault_path)))
+        tasks.append((name, loop.run_in_executor(None, _scan_vault_attachments, name, vault_path, config)))
     
     for name, task in tasks:
         new_index[name] = await task
@@ -136,18 +143,19 @@ async def build_attachment_index(vault_config: Dict[str, Dict[str, any]]) -> Non
     logger.info(f"Attachment index built: {len(attachment_index)} vaults, {total_attachments} total attachments")
 
 
-async def rescan_vault_attachments(vault_name: str, vault_path: str) -> int:
+async def rescan_vault_attachments(vault_name: str, vault_path: str, vault_cfg: dict = None) -> int:
     """Rescan attachments for a single vault.
     
     Args:
         vault_name: Name of the vault to rescan.
         vault_path: Absolute path to the vault root.
+        vault_cfg: Optional vault configuration dict with hidden files settings.
         
     Returns:
         Number of attachments indexed.
     """
     loop = asyncio.get_event_loop()
-    new_vault_index = await loop.run_in_executor(None, _scan_vault_attachments, vault_name, vault_path)
+    new_vault_index = await loop.run_in_executor(None, _scan_vault_attachments, vault_name, vault_path, vault_cfg)
     
     with _attachment_lock:
         attachment_index[vault_name] = new_vault_index
diff --git a/backend/indexer.py b/backend/indexer.py
index 9a72d5c..4c7ff11 100644
--- a/backend/indexer.py
+++ b/backend/indexer.py
@@ -61,12 +61,16 @@ def load_vault_config() -> Dict[str, Dict[str, Any]]:
     Also reads optional configuration:
     - VAULT_N_ATTACHMENTS_PATH: relative path to attachments folder
     - VAULT_N_SCAN_ATTACHMENTS: "true"/"false" to enable/disable scanning
+    - VAULT_N_INCLUDE_HIDDEN: "true"/"false" to include all hidden files/folders
+    - VAULT_N_HIDDEN_WHITELIST: comma-separated list of hidden paths to include (e.g., ".obsidian,.github")
 
     Returns:
         Dict mapping vault names to configuration dicts with keys:
         - path: filesystem path (required)
         - attachmentsPath: relative attachments folder (optional)
         - scanAttachmentsOnStartup: boolean (default True)
+        - includeHidden: boolean (default False) - include all hidden files/folders
+        - hiddenWhitelist: list of hidden paths to include even if includeHidden is False
         - type: "VAULT" or "DIR"
     """
     vaults: Dict[str, Dict[str, Any]] = {}
@@ -80,11 +84,16 @@ def load_vault_config() -> Dict[str, Dict[str, Any]]:
         # Optional configuration
         attachments_path = os.environ.get(f"VAULT_{n}_ATTACHMENTS_PATH")
         scan_attachments = os.environ.get(f"VAULT_{n}_SCAN_ATTACHMENTS", "true").lower() == "true"
+        include_hidden = os.environ.get(f"VAULT_{n}_INCLUDE_HIDDEN", "false").lower() == "true"
+        hidden_whitelist_str = os.environ.get(f"VAULT_{n}_HIDDEN_WHITELIST", "")
+        hidden_whitelist = [item.strip() for item in hidden_whitelist_str.split(",") if item.strip()]
         
         vaults[name] = {
             "path": path,
             "attachmentsPath": attachments_path,
             "scanAttachmentsOnStartup": scan_attachments,
+            "includeHidden": include_hidden,
+            "hiddenWhitelist": hidden_whitelist,
             "type": "VAULT"
         }
         n += 1
@@ -96,10 +105,16 @@ def load_vault_config() -> Dict[str, Dict[str, Any]]:
         if not name or not path:
             break
         
+        include_hidden = os.environ.get(f"DIR_{n}_INCLUDE_HIDDEN", "false").lower() == "true"
+        hidden_whitelist_str = os.environ.get(f"DIR_{n}_HIDDEN_WHITELIST", "")
+        hidden_whitelist = [item.strip() for item in hidden_whitelist_str.split(",") if item.strip()]
+        
         vaults[name] = {
             "path": path,
             "attachmentsPath": None,
             "scanAttachmentsOnStartup": False,
+            "includeHidden": include_hidden,
+            "hiddenWhitelist": hidden_whitelist,
             "type": "DIR"
         }
         n += 1
@@ -107,15 +122,49 @@ def load_vault_config() -> Dict[str, Dict[str, Any]]:
     return vaults
 
 
+def _should_include_path(rel_parts: tuple, vault_config: Dict[str, Any]) -> bool:
+    """Check if a path should be included based on hidden files configuration.
+    
+    Args:
+        rel_parts: Tuple of path parts relative to vault root
+        vault_config: Vault configuration dict with includeHidden and hiddenWhitelist
+        
+    Returns:
+        True if the path should be included, False otherwise
+    """
+    include_hidden = vault_config.get("includeHidden", False)
+    hidden_whitelist = vault_config.get("hiddenWhitelist", [])
+    
+    # Check if any part of the path starts with a dot (hidden)
+    hidden_parts = [part for part in rel_parts if part.startswith(".")]
+    
+    if not hidden_parts:
+        # No hidden parts, always include
+        return True
+    
+    if include_hidden:
+        # Include all hidden files/folders
+        return True
+    
+    # Check if any hidden part is in the whitelist
+    for hidden_part in hidden_parts:
+        if hidden_part in hidden_whitelist:
+            return True
+    
+    # Not in whitelist and includeHidden is False
+    return False
+
+
 # Regex for extracting inline #tags from markdown body (excludes code blocks)
 _INLINE_TAG_RE = re.compile(r'(?:^|\s)#([a-zA-Z][a-zA-Z0-9_/-]{1,50})', re.MULTILINE)
 # Regex patterns for stripping code blocks before inline tag extraction
-_CODE_BLOCK_RE = re.compile(r'```.*?```', re.DOTALL)
+_CODE_BLOCK_RE = re.compile(r'```[\s\S]*?```', re.MULTILINE)
 _INLINE_CODE_RE = re.compile(r'`[^`]+`')
 
 
 def _extract_tags(post: frontmatter.Post) -> List[str]:
     """Extract tags from frontmatter metadata.
+    
 
     Handles tags as comma-separated string, list, or other types.
     Strips leading ``#`` from each tag.
@@ -196,7 +245,7 @@ def parse_markdown_file(raw: str) -> frontmatter.Post:
         return frontmatter.Post(content, **{})
 
 
-def _scan_vault(vault_name: str, vault_path: str) -> Dict[str, Any]:
+def _scan_vault(vault_name: str, vault_path: str, vault_cfg: Optional[Dict[str, Any]] = None) -> Dict[str, Any]:
     """Synchronously scan a single vault directory and build file index.
 
     Walks the vault tree, reads supported files, extracts metadata
@@ -206,6 +255,7 @@ def _scan_vault(vault_name: str, vault_path: str) -> Dict[str, Any]:
     Args:
         vault_name: Display name of the vault.
         vault_path: Absolute filesystem path to the vault root.
+        vault_cfg: Optional vault configuration dict with hidden files settings.
 
     Returns:
         Dict with keys ``files`` (list), ``tags`` (counter dict), ``path`` (str), ``paths`` (list).
@@ -214,15 +264,19 @@ def _scan_vault(vault_name: str, vault_path: str) -> Dict[str, Any]:
     files: List[Dict[str, Any]] = []
     tag_counts: Dict[str, int] = {}
     paths: List[Dict[str, str]] = []
+    
+    # Default config if not provided
+    if vault_cfg is None:
+        vault_cfg = {"includeHidden": False, "hiddenWhitelist": []}
 
     if not vault_root.exists():
         logger.warning(f"Vault path does not exist: {vault_path}")
         return {"files": [], "tags": {}, "path": vault_path, "paths": []}
 
     for fpath in vault_root.rglob("*"):
-        # Skip hidden files and directories
+        # Check if path should be included based on hidden files configuration
         rel_parts = fpath.relative_to(vault_root).parts
-        if any(part.startswith(".") for part in rel_parts):
+        if not _should_include_path(rel_parts, vault_cfg):
             continue
         
         rel_path_str = str(fpath.relative_to(vault_root)).replace("\\", "/")
@@ -327,7 +381,7 @@ async def build_index(progress_callback=None) -> None:
 
     async def _process_vault(name: str, config: Dict[str, Any]):
         vault_path = config["path"]
-        vault_data = await loop.run_in_executor(None, _scan_vault, name, vault_path)
+        vault_data = await loop.run_in_executor(None, _scan_vault, name, vault_path, config)
         vault_data["config"] = config
 
         # Build lookup entries for the new vault
@@ -698,10 +752,12 @@ async def add_vault_to_index(vault_name: str, vault_path: str) -> Dict[str, Any]
         "path": vault_path,
         "attachmentsPath": None,
         "scanAttachmentsOnStartup": True,
+        "includeHidden": False,
+        "hiddenWhitelist": [],
     }
 
     loop = asyncio.get_event_loop()
-    vault_data = await loop.run_in_executor(None, _scan_vault, vault_name, vault_path)
+    vault_data = await loop.run_in_executor(None, _scan_vault, vault_name, vault_path, vault_config[vault_name])
     vault_data["config"] = vault_config[vault_name]
 
     # Build lookup entries for the new vault
diff --git a/backend/main.py b/backend/main.py
index d15a95c..c68982c 100644
--- a/backend/main.py
+++ b/backend/main.py
@@ -44,6 +44,12 @@ from backend.indexer import (
 from backend.search import search, get_all_tags, advanced_search, suggest_titles, suggest_tags
 from backend.image_processor import preprocess_images
 from backend.attachment_indexer import rescan_vault_attachments, get_attachment_stats
+from backend.vault_settings import (
+    get_vault_setting,
+    update_vault_setting,
+    get_all_vault_settings,
+    delete_vault_setting,
+)
 
 logging.basicConfig(
     level=logging.INFO,
@@ -1385,6 +1391,104 @@ async def api_attachment_stats(vault: Optional[str] = Query(None, description="V
     return {"vaults": stats}
 
 
+# ---------------------------------------------------------------------------
+# Vault Settings API — Hidden files configuration
+# ---------------------------------------------------------------------------
+
+@app.get("/api/vaults/{vault_name}/settings")
+async def api_get_vault_settings(vault_name: str, current_user=Depends(require_auth)):
+    """Get settings for a specific vault including hidden files configuration.
+    
+    Args:
+        vault_name: Name of the vault.
+        
+    Returns:
+        Dict with vault settings including includeHidden and hiddenWhitelist.
+    """
+    if vault_name not in index:
+        raise HTTPException(status_code=404, detail=f"Vault '{vault_name}' not found")
+    
+    # Get current vault config from environment
+    vault_cfg = vault_config.get(vault_name, {})
+    
+    # Get persisted settings
+    persisted = get_vault_setting(vault_name) or {}
+    
+    # Merge with defaults
+    settings = {
+        "includeHidden": vault_cfg.get("includeHidden", False),
+        "hiddenWhitelist": vault_cfg.get("hiddenWhitelist", []),
+    }
+    settings.update(persisted)
+    
+    return settings
+
+
+@app.post("/api/vaults/{vault_name}/settings")
+async def api_update_vault_settings(vault_name: str, body: dict = Body(...), current_user=Depends(require_admin)):
+    """Update settings for a specific vault.
+    
+    Args:
+        vault_name: Name of the vault.
+        body: Dict with settings to update (includeHidden, hiddenWhitelist).
+        
+    Returns:
+        Updated settings dict.
+    """
+    if vault_name not in index:
+        raise HTTPException(status_code=404, detail=f"Vault '{vault_name}' not found")
+    
+    # Validate settings
+    settings_to_update = {}
+    
+    if "includeHidden" in body:
+        if not isinstance(body["includeHidden"], bool):
+            raise HTTPException(status_code=400, detail="includeHidden must be a boolean")
+        settings_to_update["includeHidden"] = body["includeHidden"]
+    
+    if "hiddenWhitelist" in body:
+        if not isinstance(body["hiddenWhitelist"], list):
+            raise HTTPException(status_code=400, detail="hiddenWhitelist must be a list")
+        # Validate each item is a string
+        if not all(isinstance(item, str) for item in body["hiddenWhitelist"]):
+            raise HTTPException(status_code=400, detail="All hiddenWhitelist items must be strings")
+        settings_to_update["hiddenWhitelist"] = body["hiddenWhitelist"]
+    
+    # Update persisted settings
+    updated = update_vault_setting(vault_name, settings_to_update)
+    
+    # Update in-memory vault config
+    if vault_name in vault_config:
+        vault_config[vault_name].update(settings_to_update)
+    
+    logger.info(f"Updated settings for vault '{vault_name}': {settings_to_update}")
+    
+    return updated
+
+
+@app.get("/api/vaults/settings/all")
+async def api_get_all_vault_settings(current_user=Depends(require_auth)):
+    """Get settings for all vaults.
+    
+    Returns:
+        Dict mapping vault names to their settings.
+    """
+    all_settings = {}
+    
+    for vault_name in index.keys():
+        vault_cfg = vault_config.get(vault_name, {})
+        persisted = get_vault_setting(vault_name) or {}
+        
+        settings = {
+            "includeHidden": vault_cfg.get("includeHidden", False),
+            "hiddenWhitelist": vault_cfg.get("hiddenWhitelist", []),
+        }
+        settings.update(persisted)
+        all_settings[vault_name] = settings
+    
+    return all_settings
+
+
 # ---------------------------------------------------------------------------
 # Configuration API
 # ---------------------------------------------------------------------------
diff --git a/backend/vault_settings.py b/backend/vault_settings.py
new file mode 100644
index 0000000..42e9633
--- /dev/null
+++ b/backend/vault_settings.py
@@ -0,0 +1,121 @@
+"""Vault-specific settings management.
+
+Provides persistent storage for per-vault configuration like hidden files settings.
+Settings are stored in /app/data/vault_settings.json
+"""
+
+import json
+import logging
+from pathlib import Path
+from typing import Dict, Any, Optional
+import threading
+
+logger = logging.getLogger("obsigate.vault_settings")
+
+_SETTINGS_PATH = Path("/app/data/vault_settings.json")
+_settings_lock = threading.Lock()
+
+# In-memory cache of vault settings
+_vault_settings: Dict[str, Dict[str, Any]] = {}
+
+
+def load_vault_settings() -> Dict[str, Dict[str, Any]]:
+    """Load vault settings from disk.
+    
+    Returns:
+        Dict mapping vault names to their settings.
+    """
+    global _vault_settings
+    
+    with _settings_lock:
+        if _SETTINGS_PATH.exists():
+            try:
+                content = _SETTINGS_PATH.read_text(encoding="utf-8")
+                _vault_settings = json.loads(content)
+                logger.info(f"Loaded settings for {len(_vault_settings)} vaults")
+            except Exception as e:
+                logger.warning(f"Failed to load vault settings: {e}")
+                _vault_settings = {}
+        else:
+            _vault_settings = {}
+        
+        return dict(_vault_settings)
+
+
+def save_vault_settings() -> None:
+    """Persist vault settings to disk."""
+    with _settings_lock:
+        try:
+            _SETTINGS_PATH.parent.mkdir(parents=True, exist_ok=True)
+            _SETTINGS_PATH.write_text(
+                json.dumps(_vault_settings, indent=2, ensure_ascii=False),
+                encoding="utf-8"
+            )
+            logger.info(f"Saved settings for {len(_vault_settings)} vaults")
+        except Exception as e:
+            logger.error(f"Failed to save vault settings: {e}")
+            raise
+
+
+def get_vault_setting(vault_name: str) -> Optional[Dict[str, Any]]:
+    """Get settings for a specific vault.
+    
+    Args:
+        vault_name: Name of the vault.
+        
+    Returns:
+        Dict with vault settings or None if not found.
+    """
+    with _settings_lock:
+        return _vault_settings.get(vault_name)
+
+
+def update_vault_setting(vault_name: str, settings: Dict[str, Any]) -> Dict[str, Any]:
+    """Update settings for a specific vault.
+    
+    Args:
+        vault_name: Name of the vault.
+        settings: Dict with settings to update (partial update supported).
+        
+    Returns:
+        Updated settings dict for the vault.
+    """
+    with _settings_lock:
+        if vault_name not in _vault_settings:
+            _vault_settings[vault_name] = {}
+        
+        _vault_settings[vault_name].update(settings)
+        save_vault_settings()
+        
+        return dict(_vault_settings[vault_name])
+
+
+def delete_vault_setting(vault_name: str) -> bool:
+    """Delete settings for a specific vault.
+    
+    Args:
+        vault_name: Name of the vault.
+        
+    Returns:
+        True if settings were deleted, False if vault not found.
+    """
+    with _settings_lock:
+        if vault_name in _vault_settings:
+            del _vault_settings[vault_name]
+            save_vault_settings()
+            return True
+        return False
+
+
+def get_all_vault_settings() -> Dict[str, Dict[str, Any]]:
+    """Get all vault settings.
+    
+    Returns:
+        Dict mapping vault names to their settings.
+    """
+    with _settings_lock:
+        return dict(_vault_settings)
+
+
+# Initialize settings on module load
+load_vault_settings()
diff --git a/frontend/app.js b/frontend/app.js
index 25c6d88..f2da100 100644
--- a/frontend/app.js
+++ b/frontend/app.js
@@ -2968,6 +2968,7 @@
       renderConfigFilters();
       loadConfigFields();
       loadDiagnostics();
+      await loadHiddenFilesSettings();
       safeCreateIcons();
     });
 
@@ -3009,6 +3010,13 @@
     const diagBtn = document.getElementById("cfg-refresh-diag");
     if (diagBtn) diagBtn.addEventListener("click", loadDiagnostics);
 
+    // Hidden files configuration
+    const saveHiddenBtn = document.getElementById("cfg-save-hidden-files");
+    if (saveHiddenBtn) saveHiddenBtn.addEventListener("click", saveHiddenFilesSettings);
+    
+    const reindexHiddenBtn = document.getElementById("cfg-reindex-hidden");
+    if (reindexHiddenBtn) reindexHiddenBtn.addEventListener("click", reindexWithHiddenFiles);
+
     document.addEventListener("keydown", (e) => {
       if (e.key === "Escape" && modal.classList.contains("active")) {
         closeConfigModal();
@@ -3221,6 +3229,224 @@
     });
   }
 
+  // --- Hidden Files Configuration ---
+  
+  async function loadHiddenFilesSettings() {
+    const container = document.getElementById("hidden-files-vault-list");
+    if (!container) return;
+    
+    container.innerHTML = '<div style="padding:12px;color:var(--text-muted)">Chargement...</div>';
+    
+    try {
+      const settings = await api("/api/vaults/settings/all");
+      renderHiddenFilesSettings(container, settings);
+    } catch (err) {
+      console.error("Failed to load hidden files settings:", err);
+      container.innerHTML = '<div style="padding:12px;color:var(--error)">Erreur de chargement</div>';
+    }
+  }
+  
+  function renderHiddenFilesSettings(container, allSettings) {
+    container.innerHTML = "";
+    
+    if (!allVaults || allVaults.length === 0) {
+      container.innerHTML = '<div style="padding:12px;color:var(--text-muted)">Aucun vault configuré</div>';
+      return;
+    }
+    
+    allVaults.forEach(vault => {
+      const settings = allSettings[vault.name] || { includeHidden: false, hiddenWhitelist: [] };
+      
+      const vaultCard = el("div", { class: "hidden-files-vault-card", "data-vault": vault.name });
+      
+      // Vault header
+      const header = el("div", { class: "hidden-files-vault-header" }, [
+        el("h3", {}, [document.createTextNode(vault.name)]),
+        el("span", { class: "hidden-files-vault-type" }, [document.createTextNode(vault.type || "VAULT")])
+      ]);
+      
+      // Include all hidden toggle
+      const toggleRow = el("div", { class: "config-row" }, [
+        el("label", { class: "config-label", for: `hidden-include-${vault.name}` }, [
+          document.createTextNode("Inclure tous les fichiers cachés")
+        ]),
+        el("label", { class: "config-toggle" }, [
+          el("input", { 
+            type: "checkbox", 
+            id: `hidden-include-${vault.name}`,
+            "data-vault": vault.name,
+            checked: settings.includeHidden || false
+          }),
+          el("span", { class: "config-toggle-slider" })
+        ]),
+        el("span", { class: "config-hint" }, [
+          document.createTextNode("Activer pour indexer tous les fichiers et dossiers cachés (commençant par un point)")
+        ])
+      ]);
+      
+      // Whitelist section
+      const whitelistSection = el("div", { class: "hidden-files-whitelist" });
+      const whitelistLabel = el("label", { class: "config-label" }, [
+        document.createTextNode("Liste blanche (dossiers cachés spécifiques)")
+      ]);
+      const whitelistHint = el("span", { class: "config-hint", style: "display:block;margin-bottom:8px" }, [
+        document.createTextNode("Ajoutez des dossiers cachés individuels à indexer (ex: .obsidian, .github)")
+      ]);
+      
+      const whitelistItems = el("div", { class: "hidden-files-whitelist-items", id: `whitelist-items-${vault.name}` });
+      
+      // Render existing whitelist items
+      (settings.hiddenWhitelist || []).forEach(item => {
+        const itemEl = createWhitelistItem(vault.name, item);
+        whitelistItems.appendChild(itemEl);
+      });
+      
+      // Add new item input
+      const addRow = el("div", { class: "hidden-files-add-row" }, [
+        el("input", { 
+          type: "text", 
+          class: "config-input",
+          id: `whitelist-input-${vault.name}`,
+          placeholder: "Ex: .obsidian"
+        }),
+        el("button", { 
+          class: "config-btn-add",
+          type: "button",
+          "data-vault": vault.name
+        }, [document.createTextNode("Ajouter")])
+      ]);
+      
+      whitelistSection.appendChild(whitelistLabel);
+      whitelistSection.appendChild(whitelistHint);
+      whitelistSection.appendChild(whitelistItems);
+      whitelistSection.appendChild(addRow);
+      
+      vaultCard.appendChild(header);
+      vaultCard.appendChild(toggleRow);
+      vaultCard.appendChild(whitelistSection);
+      
+      container.appendChild(vaultCard);
+      
+      // Event listeners
+      const addBtn = addRow.querySelector("button");
+      const input = addRow.querySelector("input");
+      
+      addBtn.addEventListener("click", () => addWhitelistItem(vault.name));
+      input.addEventListener("keypress", (e) => {
+        if (e.key === "Enter") addWhitelistItem(vault.name);
+      });
+    });
+  }
+  
+  function createWhitelistItem(vaultName, itemValue) {
+    const item = el("div", { class: "hidden-files-whitelist-item" }, [
+      el("span", { class: "whitelist-item-text" }, [document.createTextNode(itemValue)]),
+      el("button", { 
+        class: "whitelist-item-remove",
+        type: "button",
+        title: "Supprimer",
+        "data-vault": vaultName,
+        "data-item": itemValue
+      }, [document.createTextNode("×")])
+    ]);
+    
+    const removeBtn = item.querySelector("button");
+    removeBtn.addEventListener("click", () => {
+      item.remove();
+    });
+    
+    return item;
+  }
+  
+  function addWhitelistItem(vaultName) {
+    const input = document.getElementById(`whitelist-input-${vaultName}`);
+    const container = document.getElementById(`whitelist-items-${vaultName}`);
+    
+    if (!input || !container) return;
+    
+    const value = input.value.trim();
+    if (!value) return;
+    
+    // Validate format (should start with a dot)
+    if (!value.startsWith(".")) {
+      showToast("Le nom doit commencer par un point (ex: .obsidian)", "error");
+      return;
+    }
+    
+    // Check for duplicates
+    const existing = Array.from(container.querySelectorAll(".whitelist-item-text"))
+      .map(el => el.textContent);
+    if (existing.includes(value)) {
+      showToast("Cet élément existe déjà", "error");
+      return;
+    }
+    
+    const item = createWhitelistItem(vaultName, value);
+    container.appendChild(item);
+    input.value = "";
+  }
+  
+  async function saveHiddenFilesSettings() {
+    const btn = document.getElementById("cfg-save-hidden-files");
+    if (btn) { btn.disabled = true; btn.textContent = "Sauvegarde..."; }
+    
+    try {
+      const vaultCards = document.querySelectorAll(".hidden-files-vault-card");
+      const promises = [];
+      
+      vaultCards.forEach(card => {
+        const vaultName = card.dataset.vault;
+        const includeHidden = document.getElementById(`hidden-include-${vaultName}`)?.checked || false;
+        
+        const whitelistItems = Array.from(
+          document.querySelectorAll(`#whitelist-items-${vaultName} .whitelist-item-text`)
+        ).map(el => el.textContent);
+        
+        const settings = {
+          includeHidden,
+          hiddenWhitelist: whitelistItems
+        };
+        
+        promises.push(
+          fetch(`/api/vaults/${encodeURIComponent(vaultName)}/settings`, {
+            method: "POST",
+            headers: { "Content-Type": "application/json" },
+            body: JSON.stringify(settings)
+          })
+        );
+      });
+      
+      await Promise.all(promises);
+      showToast("Paramètres des fichiers cachés sauvegardés", "success");
+    } catch (err) {
+      console.error("Failed to save hidden files settings:", err);
+      showToast("Erreur de sauvegarde", "error");
+    } finally {
+      if (btn) { btn.disabled = false; btn.textContent = "Sauvegarder les paramètres"; }
+    }
+  }
+  
+  async function reindexWithHiddenFiles() {
+    const btn = document.getElementById("cfg-reindex-hidden");
+    if (btn) { btn.disabled = true; btn.textContent = "Réindexation..."; }
+    
+    try {
+      // First save the settings
+      await saveHiddenFilesSettings();
+      
+      // Then trigger reindex
+      await api("/api/index/reload");
+      showToast("Réindexation avec nouveaux paramètres terminée", "success");
+      loadDiagnostics();
+      await Promise.all([loadVaults(), loadTags()]);
+    } catch (err) {
+      console.error("Reindex with hidden files error:", err);
+      showToast("Erreur de réindexation", "error");
+    } finally {
+      if (btn) { btn.disabled = false; btn.textContent = "Réindexer avec nouveaux paramètres"; }
+    }
+  }
+
   function renderConfigFilters() {
     const config = TagFilterService.getConfig();
     const filters = config.tagFilters || TagFilterService.defaultFilters;
diff --git a/frontend/index.html b/frontend/index.html
index b94bbed..36d75cf 100644
--- a/frontend/index.html
+++ b/frontend/index.html
@@ -548,6 +548,21 @@
             </div>
           </section>
 
+          <!-- Hidden Files/Folders Configuration -->
+          <section class="config-section">
+            <h2>📁 Fichiers et dossiers cachés</h2>
+            <p class="config-description">Configurez la prise en charge des fichiers et dossiers cachés (commençant par un point) pour chaque vault. Vous pouvez activer tous les fichiers cachés ou ajouter des dossiers spécifiques à une liste blanche.</p>
+            
+            <div id="hidden-files-vault-list">
+              <!-- Vault-specific settings will be injected here -->
+            </div>
+            
+            <div class="config-actions-row" style="margin-top: 16px;">
+              <button class="config-btn-save" id="cfg-save-hidden-files">Sauvegarder les paramètres</button>
+              <button class="config-btn-secondary" id="cfg-reindex-hidden">Réindexer avec nouveaux paramètres</button>
+            </div>
+          </section>
+
           <!-- Diagnostics -->
           <section class="config-section">
             <h2>Diagnostics</h2>
diff --git a/frontend/style.css b/frontend/style.css
index fc74ab2..85fdbfa 100644
--- a/frontend/style.css
+++ b/frontend/style.css
@@ -3408,6 +3408,99 @@ body.resizing-v {
   background: #22c55e;
 }
 
+/* ---------------------------------------------------------------------------
+   Hidden Files Configuration
+   --------------------------------------------------------------------------- */
+.hidden-files-vault-card {
+  background: var(--bg-secondary);
+  border: 1px solid var(--border);
+  border-radius: 8px;
+  padding: 16px;
+  margin-bottom: 16px;
+}
+
+.hidden-files-vault-header {
+  display: flex;
+  align-items: center;
+  justify-content: space-between;
+  margin-bottom: 16px;
+  padding-bottom: 12px;
+  border-bottom: 1px solid var(--border);
+}
+
+.hidden-files-vault-header h3 {
+  font-size: 1rem;
+  font-weight: 600;
+  color: var(--text-primary);
+  margin: 0;
+}
+
+.hidden-files-vault-type {
+  font-size: 0.75rem;
+  padding: 2px 8px;
+  background: var(--tag-bg);
+  color: var(--tag-text);
+  border-radius: 4px;
+  font-family: var(--mono);
+}
+
+.hidden-files-whitelist {
+  margin-top: 16px;
+  padding-top: 16px;
+  border-top: 1px solid var(--border);
+}
+
+.hidden-files-whitelist-items {
+  display: flex;
+  flex-wrap: wrap;
+  gap: 8px;
+  margin-bottom: 12px;
+  min-height: 32px;
+}
+
+.hidden-files-whitelist-item {
+  display: inline-flex;
+  align-items: center;
+  gap: 6px;
+  padding: 4px 8px 4px 12px;
+  background: var(--tag-bg);
+  color: var(--tag-text);
+  border-radius: 6px;
+  font-size: 0.875rem;
+  font-family: var(--mono);
+  border: 1px solid color-mix(in srgb, var(--tag-text) 30%, transparent);
+}
+
+.whitelist-item-text {
+  user-select: none;
+}
+
+.whitelist-item-remove {
+  background: none;
+  border: none;
+  color: var(--text-muted);
+  cursor: pointer;
+  font-size: 1.2rem;
+  line-height: 1;
+  padding: 0 4px;
+  transition: color 150ms ease;
+}
+
+.whitelist-item-remove:hover {
+  color: var(--danger);
+}
+
+.hidden-files-add-row {
+  display: flex;
+  gap: 8px;
+  align-items: center;
+}
+
+.hidden-files-add-row .config-input {
+  flex: 1;
+  max-width: 300px;
+}
+
 /* ---------------------------------------------------------------------------
    Utility — hidden class
    --------------------------------------------------------------------------- */