fix(api): avoid committing inside RAG pipeline DSL service.

[FFXN]

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Summary

Due to multiple commits in sessionmaker, the transaction is closed early.

Screenshots

Before	After
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Checklist

• This change requires a documentation update, included: Dify Document
• I understand that this PR may be closed in case there was no previous discussion or issues. (This doesn't apply to typos!)
• I've added a test for each change that was introduced, and I tried as much as possible to make a single atomic change.
• I've updated the documentation accordingly.
• I ran make lint && make type-check (backend) and cd web && pnpm exec vp staged (frontend) to appease the lint gods

[github-actions]

Pyrefly Type Coverage

Metric	Base	PR	Delta
Type coverage	0.00%	43.65%	+43.65%
Strict coverage	0.00%	43.18%	+43.18%
Typed symbols	0	22,044	+22,044
Untyped symbols	0	28,770	+28,770
Modules	0	2552	+2,552