修复：输出前缀绑定替换保留原引号，避免 Python -c 字符串字面量变裸标识符（zh01 NameError）

tests/unit/test_extension_stage_lightweight_runtime_package.py

@@ -1528,3 +1528,31 @@ def test_replay_isolates_symlink_input_before_source_overwrite(
         }
     ]
     assert result["execution_work_tree"]["Ft.input.txt"]["type"] == "regular"
+
+
+def test_shell_word_replacement_preserves_python_string_literal_quotes() -> None:
+    """zh01 回归：python -c 里带引号的输出路径被前缀替换后必须保留引号。
+
+    替换前：SeqIO.write(...,'combined.pep.fasta','fasta')
+    若用 shlex.quote 替换会变成 SeqIO.write(...,output.fasta,'fasta')
+    → Python 报 NameError: name 'output' is not defined。
+    """
+    pattern = runtime_module._shell_word_pattern("combined.pep.fasta")
+    replace = runtime_module._shell_word_replacement("output.fasta")
+    source = (
+        "python -c \"from Bio import SeqIO; "
+        "SeqIO.write(list(SeqIO.parse('Ft.SPL.pep.fasta','fasta')),"
+        "'combined.pep.fasta','fasta')\" && "
+        "muscle -in combined.pep.fasta -out combined.pep.mfa"
+    )
+    updated, count = pattern.subn(replace, source)
+    assert count == 2
+    assert "'output.fasta'" in updated
+    assert "'combined.pep.fasta'" not in updated
+    # 无引号的 shell 单词路径不受影响（不引入引号）
+    shell_text = "muscle -in combined.pep.mfa -out combined.pep.mfa2"
+    updated_shell, shell_count = runtime_module._shell_word_pattern(
+        "combined.pep.mfa"
+    ).subn(runtime_module._shell_word_replacement("output.mfa"), shell_text)
+    assert shell_count == 1
+    assert "-in output.mfa" in updated_shell