🛠 refactor: Ensure File Deletions, File Naming, and Agent Resource Updates

[danny-avila]

Summary

• Only re-throw vector deletion if status code is error and not 404 (not found)
• Prefix filenames with the file ID during upload to ensure uniqueness when saving files.
• Remove the version specification from deploy-compose.yml to simplify deployment settings.
• Update addAgentResourceFile to initialize missing tool resource arrays, ensuring robust agent resource updates and expanding test coverage.
• Add an uploads directory mapping in both Docker Compose files to persist user-uploaded files for docker deployments
• Refine error logging in file upload and processing functions by leveraging a centralized logAxiosError utility to reduce verbosity.
• Only shows top 5 results for file search, instead of 5 per file attached

Closes #5298
Closes #5312

Change Type

• Bug fix (non-breaking change which fixes an issue)

Testing
I verified these changes by running unit and integration tests. I also manually checked that:

• File uploads are assigned unique filenames and stored correctly.
• Agent resource updates behave as expected through the added test suite.
• Warnings and error logs appear appropriately in API endpoints.
• Docker Compose correctly mounts the uploads directory.

Checklist

• My code adheres to this project's style guidelines.
• I have performed a self-review of my own code.
• I have commented in any complex areas of the code.
• My changes do not introduce new warnings.
• I have written tests demonstrating that my changes are effective.
• Local unit tests pass with my changes.
• Any changes dependent on mine have been merged and published in downstream modules.