Investigate and resolve runtime warnings and API deprecations

Summary

Review Vizably's runtime logs to identify and resolve deprecated API usage, repeated failed requests, unexpected warnings, and other unnecessary log noise.

Problem

Recent runtime logs show several messages that may indicate outdated API usage or underlying implementation issues, including:

• GitHub API deprecation warnings for repository creation requests.
• Repeated 404 responses when looking up scan/manifest files.
• Repository initialization behaviour that may trigger unnecessary requests.
• Other warnings or errors that provide little actionable information or may indicate avoidable failures.

These should be investigated individually to distinguish expected behaviour from actual implementation issues.

Investigation Areas

GitHub API

• Identify the source of deprecated GitHub API requests.
• Update affected Octokit requests to use the current GitHub API conventions.
• Confirm that the updated requests continue to work correctly.

Manifest and Scan Lookups

• Investigate repeated 404 responses for expected files such as vizably.json and scan-related files.
• Determine whether the requests are expected, unnecessary, or caused by incorrect repository initialization.
• Prevent unnecessary repeated requests where appropriate.

Repository Initialization

• Review how scan repositories and required files are initialized.
• Confirm that initialization does not produce avoidable API requests or errors.

Runtime Logging

• Identify warnings and errors that are expected and should be handled appropriately.
• Remove or reduce unnecessary log noise.
• Preserve logs that are useful for debugging genuine failures.

Acceptance Criteria

• GitHub API deprecation warnings are resolved or documented with a clear reason if they cannot be removed.
• The source of repeated 404 requests is identified and addressed where appropriate.
• Repository initialization behaviour is verified and corrected if necessary.
• Unnecessary runtime warnings and errors are reduced.
• Meaningful errors remain visible and actionable.
• Existing GitHub storage and scan functionality continues to work after the changes.
• Runtime logs are reviewed after the changes to confirm the identified issues no longer occur unnecessarily.

Related Work

This issue should be considered complete only after the relevant runtime behaviour has been verified locally.