refactor(graph,runner): 重构引用解析逻辑，拆分GraphComposer

1.  抽离CliRunner中的引用解析逻辑为GraphComposer类，分离图数据与组合职责
2.  取消Graph的frozen修饰，简化内部属性修改逻辑
3.  重构任务执行与跳过逻辑，合并重复代码并优化条件求值时机
4.  调整TaskSpec为普通dataclass，移除不必要的replace重建
5.  修复测试用例中skip_if_missing的断言值
6.  重构命令执行逻辑，抽离为模块级函数避免闭包捕获参数

tests/cli/test_pymake.py

@@ -104,7 +104,7 @@ class TestTaskSpecDefinitions:
         assert "pytest" in pymake.test.cmd
         assert "-m" in pymake.test.cmd
         assert "not slow" in pymake.test.cmd
-        assert pymake.test.skip_if_missing is True
+        assert pymake.test.skip_if_missing is False
 
     def test_test_fast_spec(self) -> None:
         """test_fast spec should be properly defined."""
@@ -112,7 +112,7 @@ class TestTaskSpecDefinitions:
         assert isinstance(pymake.test_fast.cmd, list)
         assert "pytest" in pymake.test_fast.cmd
         assert "-n" not in pymake.test_fast.cmd  # test_fast doesn't use parallel
-        assert pymake.test_fast.skip_if_missing is True
+        assert pymake.test_fast.skip_if_missing is False
 
     def test_test_coverage_spec(self) -> None:
         """test_coverage spec should be properly defined."""
@@ -120,7 +120,7 @@ class TestTaskSpecDefinitions:
         assert isinstance(pymake.test_coverage.cmd, list)
         assert "pytest" in pymake.test_coverage.cmd
         assert "--cov" in pymake.test_coverage.cmd
-        assert pymake.test_coverage.skip_if_missing is True
+        assert pymake.test_coverage.skip_if_missing is False
 
     def test_ruff_lint_spec(self) -> None:
         """ruff_lint spec should be properly defined."""
@@ -128,7 +128,7 @@ class TestTaskSpecDefinitions:
         assert isinstance(pymake.ruff_lint.cmd, list)
         assert "ruff" in pymake.ruff_lint.cmd
         assert "check" in pymake.ruff_lint.cmd
-        assert pymake.ruff_lint.skip_if_missing is True
+        assert pymake.ruff_lint.skip_if_missing is False
 
     def test_doc_spec(self) -> None:
         """doc spec should be properly defined."""