fix: fix kcl.yaml missing bug when kcl run

[zong-zhe]

1. Does this PR affect any open issues?(Y/N) and add issue references (e.g. "fix #123", "re #123".):

• N
• Y

re #443

2. What is the scope of this PR (e.g. component or file name):

3. Provide a description of the PR(e.g. more details, effects, motivations or doc link):

• Affects user behaviors
• Contains syntax changes
• Contains variable changes
• Contains experimental features
• Performance regression: Consumes more CPU
• Performance regression: Consumes more Memory
• Other

4. Are there any breaking changes?(Y/N) and describe the breaking changes(e.g. more details, motivations or doc link):

• N
• Y

5. Are there test cases for these changes?(Y/N) select and add more details, references or doc links:

• Unit test
• Integration test
• Benchmark (add benchmark stats below)
• Manual test (add detailed scripts or steps below)
• Other