Silent except-pass swallows real failures: plugin tool registration, shell reader threads, and file-modification helpers

Files (theme: silent failure of core wiring):

1. code_puppy/tools/__init__.py:204-207 - _load_plugin_tools():

    except Exception:
        # Don't let plugin failures break core functionality
        pass

If on_register_tools() blows up, ALL plugin-provided tools silently vanish from TOOL_REGISTRY. The agent then emits "Unknown tool 'X' requested, skipping..." with no hint of the root cause. At minimum emit_warning/logger.exception here.

2. code_puppy/tools/command_runner.py - the read_stdout/read_stderr reader threads end in stacked

        except (ValueError, OSError):
            pass
        except Exception:
            pass

(lines ~760-775 and ~830-840). The second handler swallows everything including programming errors in the reader; a reader thread dying mid-stream means truncated output reported as a clean result. Log the exception (even debug-level) before exiting the thread, and drop the redundant first handler.

3. code_puppy/tools/file_modifications.py - _delete_snippet_from_file / _replace_in_file end with except Exception as exc: return {"error": str(exc), "diff": diff_text} - acceptable as a tool boundary, but unlike _write_to_file they don't call _log_error, so tracebacks for genuine bugs are lost. Inconsistent error-handling strategy within one module; add _log_error(..., exc) to match.

Roughly 40 except Exception: handlers exist in tools/ alone; most are fine (UI best-effort), but the three above hide real wiring/IO failures. Errors should never pass silently unless explicitly silenced - these aren't explicit, they're invisible.

Filed by Zen Reviewer B (code-puppy-60635a)

Start with _load_plugin_tools() in code_puppy/tools/init.py, the read_stdout/read_stderr threads in code_puppy/tools/command_runner.py, and _delete_snippet_from_file/_replace_in_file in code_puppy/tools/file_modifications.py. Trace how each exception is currently handled, then verify that plugin, reader-thread, and file-helper failures are no longer silent while the existing tool-boundary error results remain intact.