fix: remove 115 verified dead code symbols across 46 production files

Automated dead code audit using vulture + coverage.py + ast-grep intersection,
confirmed by Opus deep verification pass. Every symbol verified to have zero
production callers (test imports excluded from reachability analysis).

Removes ~1,534 lines of dead production code across 46 files and ~1,382 lines
of stale test code. 3 entire files deleted (agent/builtin_memory_provider.py,
hermes_cli/checklist.py, tests/hermes_cli/test_setup_model_selection.py).

Co-authored-by: alt-glitch <balyan.sid@gmail.com>

tools/environments/base.py

@@ -547,9 +547,3 @@ class BaseEnvironment(ABC):
 
         return _transform_sudo_command(command)
 
-    def _timeout_result(self, timeout: int | None) -> dict:
-        """Standard return dict when a command times out."""
-        return {
-            "output": f"Command timed out after {timeout or self.timeout}s",
-            "returncode": 124,
-        }