fix(api): handle missing upload_file_id for tool_file messages

[laipz8200]

Checklist:

Important

Please review the checklist below before submitting your pull request.

• Please open an issue before creating a PR or link to an existing issue
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I ran dev/reformat(backend) and cd web && npx lint-staged(frontend) to appease the lint gods

Description

• Ensure upload_file_id is set using the URL if it's missing for tool_file transfer method.
• Add a session commit after processing message files to persist changes.

Fixes

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update, included: Dify Document
• Improvement, including but not limited to code refactoring, performance optimization, and UI/UX improvement
• Dependency upgrade

Testing Instructions

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

• Test A
• Test B

[GarfieldDai]

LGTM