fixes for sync

src/basic_memory/cli/main.py

@@ -14,7 +14,7 @@ __all__ = ["init", "status", "sync"]
 from basic_memory.config import config
 
 
-def setup_logging(home_dir: str = config.home, log_file: str = "basic-memory-tools.log"):
+def setup_logging(home_dir: str = config.home, log_file: str = "./basic-memory/basic-memory-tools.log"):
     """Configure logging for the application."""
 
     # Remove default handler and any existing handlers

src/basic_memory/mcp/tools/discussion.py

@@ -10,7 +10,6 @@ from basic_memory.schemas.memory import GraphContext, MemoryUrl
 
 
 @mcp.tool(
-    name="Build Context",
     description="Build context from a memory:// URI to continue conversations naturally.",
 )
 async def build_context(

src/basic_memory/models/knowledge.py

@@ -30,13 +30,16 @@ def generate_permalink(file_path: str) -> str:
         file_path: Original file path
         
     Returns:
-        Normalized permalink that matches validation rules
+        Normalized permalink that matches validation rules. Converts spaces and underscores
+        to hyphens for consistency.
         
     Examples:
         >>> generate_permalink("docs/My Feature.md")
         'docs/my-feature'
         >>> generate_permalink("specs/API (v2).md")
         'specs/api-v2'
+        >>> generate_permalink("design/unified_model_refactor.md")
+        'design/unified-model-refactor'
     """
     # Remove extension
     base = os.path.splitext(file_path)[0]
@@ -47,8 +50,11 @@ def generate_permalink(file_path: str) -> str:
     # Convert to lowercase
     lower_text = ascii_text.lower()
     
-    # Replace spaces and invalid chars with hyphens
-    clean_text = re.sub(r'[^a-z0-9/\-_]', '-', lower_text)
+    # First replace underscores with hyphens
+    text_with_hyphens = lower_text.replace('_', '-')
+    
+    # Replace remaining invalid chars with hyphens
+    clean_text = re.sub(r'[^a-z0-9/\-]', '-', text_with_hyphens)
     
     # Collapse multiple hyphens
     clean_text = re.sub(r'-+', '-', clean_text)
@@ -130,17 +136,17 @@ class Entity(Base):
         
         Requirements:
         1. Must be valid URI path component
-        2. Only lowercase letters, numbers, hyphens, and underscores
+        2. Only lowercase letters, numbers, and hyphens (no underscores)
         3. Path segments separated by forward slashes
         4. No leading/trailing hyphens in segments
         """
         if not value:
             raise ValueError("Permalink must not be None")
         
-        if not re.match(r'^[a-z0-9][a-z0-9\-_/]*[a-z0-9]$', value):
+        if not re.match(r'^[a-z0-9][a-z0-9\-/]*[a-z0-9]$', value):
             raise ValueError(
                 f"Invalid permalink format: {value}. "
-                "Use only lowercase letters, numbers, hyphens, and underscores."
+                "Use only lowercase letters, numbers, and hyphens."
             )
         return value
 

src/basic_memory/repository/search_repository.py

@@ -74,10 +74,16 @@ class SearchRepository:
             await session.commit()
 
     def _quote_search_term(self, term: str) -> str:
-        """Add quotes if term contains special characters or /.
-            For FTS5, phrases with / need to be quoted to be treated as a single token.
+        """Add quotes if term contains special characters.
+        For FTS5, special characters and phrases need to be quoted to be treated as a single token.
         """
-        if '/' in term or '*' in term or any(c in term for c in "-"):
+        # List of special characters that need quoting
+        special_chars = ['/', '*', '-', '.', ' ', '(', ')', '[', ']', '"', "'"]
+        
+        # Check if term contains any special characters
+        if any(c in term for c in special_chars):
+            # If the term already contains quotes, escape them
+            term = term.replace('"', '""')
             return f'"{term}"'
         return term
 
@@ -229,4 +235,4 @@ class SearchRepository:
             else:
                 result = await session.execute(query)
             logger.debug("Query executed successfully")
-            return result
+            return result

src/basic_memory/services/link_resolver.py

@@ -123,5 +123,5 @@ class LinkResolver():
             scored_results.append((score, result))
 
         # Sort by score (lowest first) and return best
-        scored_results.sort()
+        scored_results.sort(key=lambda x: x[0], reverse=True)
         return scored_results[0][1]