Standardize matching test files structure, add test_main.py and test_commands.py, and update GEMINI.md

tests/test_forensics.py

@@ -295,29 +295,3 @@ def test_forensics_flag_detect_cli_not_found():
     result = runner.invoke(forensics_group, ["flag-detect", str(test_file)])
     assert result.exit_code == 0
     assert "No flag patterns found" in result.output
-
-def test_set_flag_format_cli():
-    """
-    Verifies that 'set-flag-format' CLI command writes the pattern to config.toml.
-    """
-    from ctf.commands import set_flag_format
-    from ctf.utils import load_config
-    
-    runner = CliRunner()
-    config_file = Path("/home/venus/code/ctf/config.toml")
-    
-    # Save the original config to restore later
-    original_config = load_config(str(config_file))
-    
-    try:
-        result = runner.invoke(set_flag_format, ["TEST_FLAG{[a-z]+}"])
-        assert result.exit_code == 0
-        assert "Flag format set to" in result.output
-        
-        # Verify it was written to config.toml
-        updated_config = load_config(str(config_file))
-        assert updated_config["Competition"]["flag_format"] == "TEST_FLAG{[a-z]+}"
-    finally:
-        # Restore original config
-        from ctf.utils import write_config
-        write_config(original_config, str(config_file))