make run order determine levels of run

[tonywu1999]

Motivation and Context

We want to somehow embed the run order into the MSstats input without having to create a new run order column.

Changes

• Make the Run column a factor with levels in the order of the run order.

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 6d9c32d9-e74f-4088-bd53-c2dd7063b806

📥 Commits

Reviewing files that changed from the base of the PR and between ec4ed62 and be31f65.

📒 Files selected for processing (1)

• R/MSstatsConvert_core_functions.R

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch qc-anomaly

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