Simplify code documentation, remove organism terminology

- Remove biological metaphors from docstrings (organism, sensory, genetic, nutrient, etc.)
- Simplify documentation to be minimal and structured for fast model parsing
- Complete SQLite to JSON storage migration (project_manager.py, json_store.py)
- Add Integrations and IntegrationHealth classes to json_store.py
- Add kill_port() function to server.py for port conflict handling
- All 33 tests pass

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

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

tools/api/services/project_manager.py

@@ -248,48 +248,14 @@ class ProjectManager:
 
     def _update_root_path(self, project_id: str, root_path: str) -> None:
         """
-        Update root_path in database.
-
-        Uses raw SQL since the column may not be in the existing model.
+        Update root_path in JSON storage.
         """
-        from storage.database import get_connection
-
-        with get_connection() as conn:
-            # Ensure column exists
-            try:
-                conn.execute("""
-                    ALTER TABLE projects ADD COLUMN root_path TEXT DEFAULT ''
-                """)
-                logger.info("Added root_path column to projects table")
-            except Exception:
-                # Column already exists
-                pass
-
-            # Update the value
-            conn.execute(
-                "UPDATE projects SET root_path = ? WHERE id = ?",
-                (root_path, project_id)
-            )
+        self.db.update(project_id, root_path=root_path)
 
     @staticmethod
     def ensure_schema():
         """
-        Ensure database schema has root_path column.
-
-        Call this on startup to migrate existing databases.
+        Legacy schema migration - no longer needed with JSON storage.
+        Kept for API compatibility.
         """
-        from storage.database import get_connection
-
-        with get_connection() as conn:
-            cursor = conn.cursor()
-            # Check if column exists
-            cursor.execute("PRAGMA table_info(projects)")
-            columns = [col[1] for col in cursor.fetchall()]
-
-            if 'root_path' not in columns:
-                cursor.execute("""
-                    ALTER TABLE projects ADD COLUMN root_path TEXT DEFAULT ''
-                """)
-                logger.info("Migration: Added root_path column to projects table")
-            else:
-                logger.debug("Schema check: root_path column exists")
+        logger.debug("Schema check: Using JSON storage, no migration needed")