fix(mcp-kb): address critical issues from deep review

- Fix SQL HAVING clause bug by using CTE approach (closes #73)
- Add /mcp JSON-RPC 2.0 endpoint for tool execution (closes #74)
- Add /mcp/tools endpoint for tool discovery (closes #75)
- Add content size limits to prevent DoS attacks (closes #78)
- Add comprehensive tests for new endpoints

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

mcp-servers/knowledge-base/database.py

@@ -345,8 +345,9 @@ class DatabaseManager:
         """
         try:
             async with self.acquire() as conn:
-                # Build query with optional filters
-                query = """
+                # Build query with optional filters using CTE to filter by similarity
+                # We use a CTE to compute similarity once, then filter in outer query
+                inner_query = """
                     SELECT
                         id, project_id, collection, content, embedding,
                         chunk_type, source_path, start_line, end_line,
@@ -361,18 +362,21 @@ class DatabaseManager:
                 param_idx = 3
 
                 if collection:
-                    query += f" AND collection = ${param_idx}"
+                    inner_query += f" AND collection = ${param_idx}"
                     params.append(collection)
                     param_idx += 1
 
                 if file_types:
                     file_type_values = [ft.value for ft in file_types]
-                    query += f" AND file_type = ANY(${param_idx})"
+                    inner_query += f" AND file_type = ANY(${param_idx})"
                     params.append(file_type_values)
                     param_idx += 1
 
-                query += f"""
-                    HAVING 1 - (embedding <=> $1) >= ${param_idx}
+                # Wrap in CTE and filter by threshold in outer query
+                query = f"""
+                    WITH scored AS ({inner_query})
+                    SELECT * FROM scored
+                    WHERE similarity >= ${param_idx}
                     ORDER BY similarity DESC
                     LIMIT ${param_idx + 1}
                 """