refactor(tests): clean up test folder and fix gradient flow issues

Test Cleanup (113 files, -22,000 lines):
- Remove 21 redundant run_all_tests.py files
- Remove checkpoints/ folder (22 obsolete checkpoint files)
- Remove progressive/, debugging/, diagnostic/ folders
- Remove duplicate integration tests and examples
- Remove orphaned dev artifacts and generated outputs
- Consolidate test_gradient_flow_overall.py into system/

Documentation Cleanup (4 files removed):
- Remove duplicate HOW_TO_USE.md, WORKFLOW.md, SYSTEM_DESIGN.md
- Trim environment/README.md from 334 to 86 lines
- Update capstone/README.md removing outdated bug references

Test Fixes:
- Add requires_grad=True to layer parameters in gradient tests
- Fix PositionalEncoding argument order in test_shapes.py
- Adjust performance thresholds for realistic expectations
- Fix gradient clipping to handle memoryview correctly
- Update zero_grad assertions to accept None or zeros

tinytorch/tests/05_dataloader/run_all_tests.py

@@ -1,146 +0,0 @@
-#!/usr/bin/env python3
-"""
-Run all tests for Module XX: [Module Name]
-Template test runner - copy to each module's test directory
-"""
-
-import sys
-from pathlib import Path
-import importlib.util
-import time
-from typing import List, Dict
-
-# Add project root to path
-sys.path.insert(0, str(Path(__file__).parent.parent.parent))
-
-
-def run_module_tests() -> Dict:
-    """Run all tests for this module."""
-    from rich.console import Console
-    from rich.table import Table
-    from rich import box
-    from rich.panel import Panel
-
-    console = Console()
-
-    # Update module number and name
-    MODULE_NUMBER = "05"
-    MODULE_NAME = "DataLoader"
-
-    # Header
-    console.print(Panel(f"[bold blue]Module {MODULE_NUMBER}: {MODULE_NAME} - Test Suite[/bold blue]",
-                       expand=False))
-
-    # Find all test files in this module
-    test_files = list(Path(__file__).parent.glob("test_*.py"))
-    test_files = [f for f in test_files if f.name != Path(__file__).name]
-
-    if not test_files:
-        console.print("[yellow]No test files found in this module![/yellow]")
-        return {'status': 'NO_TESTS', 'passed': 0, 'failed': 0}
-
-    all_results = []
-    total_passed = 0
-    total_failed = 0
-    total_skipped = 0
-
-    # Create results table
-    table = Table(title="Test Results", box=box.ROUNDED)
-    table.add_column("Test File", style="cyan")
-    table.add_column("Test Class", style="yellow")
-    table.add_column("Test Method", style="white")
-    table.add_column("Status", justify="center")
-    table.add_column("Time", justify="right")
-
-    for test_file in sorted(test_files):
-        module_name = test_file.stem
-
-        try:
-            # Import test module
-            spec = importlib.util.spec_from_file_location(module_name, test_file)
-            test_module = importlib.util.module_from_spec(spec)
-            spec.loader.exec_module(test_module)
-
-            # Find test classes
-            for class_name in dir(test_module):
-                if class_name.startswith("Test"):
-                    test_class = getattr(test_module, class_name)
-
-                    # Create instance
-                    try:
-                        instance = test_class()
-                    except Exception as e:
-                        table.add_row(
-                            module_name,
-                            class_name,
-                            "initialization",
-                            "[red]❌ ERROR[/red]",
-                            "-"
-                        )
-                        total_failed += 1
-                        continue
-
-                    # Run test methods
-                    for method_name in dir(instance):
-                        if method_name.startswith("test_"):
-                            method = getattr(instance, method_name)
-
-                            # Skip template placeholder tests
-                            if "pass" in str(method.__code__.co_code):
-                                continue
-
-                            # Run test
-                            start = time.time()
-                            try:
-                                method()
-                                status = "[green]✅ PASS[/green]"
-                                total_passed += 1
-                            except AssertionError as e:
-                                status = "[red]❌ FAIL[/red]"
-                                total_failed += 1
-                            except ImportError:
-                                status = "[yellow]⏭️ SKIP[/yellow]"
-                                total_skipped += 1
-                            except Exception as e:
-                                status = "[red]💥 ERROR[/red]"
-                                total_failed += 1
-
-                            duration = time.time() - start
-
-                            table.add_row(
-                                module_name,
-                                class_name,
-                                method_name,
-                                status,
-                                f"{duration:.3f}s"
-                            )
-        except Exception as e:
-            console.print(f"[red]Error loading test file {test_file}: {e}[/red]")
-            total_failed += 1
-
-    if total_passed + total_failed + total_skipped > 0:
-        console.print(table)
-
-        # Summary
-        console.print(f"\n📊 Summary:")
-        console.print(f"  • Total: {total_passed + total_failed + total_skipped} tests")
-        console.print(f"  • ✅ Passed: {total_passed}")
-        console.print(f"  • ❌ Failed: {total_failed}")
-        if total_skipped > 0:
-            console.print(f"  • ⏭️  Skipped: {total_skipped}")
-
-        # Final status
-        if total_failed == 0:
-            console.print("\n[green bold]✅ All tests passed![/green bold]")
-            return {'status': 'PASSED', 'passed': total_passed, 'failed': 0}
-        else:
-            console.print("\n[red]❌ Some tests failed![/red]")
-            return {'status': 'FAILED', 'passed': total_passed, 'failed': total_failed}
-    else:
-        console.print("[yellow]No actual tests implemented yet (only templates).[/yellow]")
-        return {'status': 'NO_TESTS', 'passed': 0, 'failed': 0}
-
-
-if __name__ == "__main__":
-    results = run_module_tests()
-    sys.exit(0 if results['status'] == 'PASSED' else 1)