refactor(storage): ensure output dir is cleared before each run

[Koech01]

Summary

This PR ensures that the output directory is cleared before each notebook run. This prevents stale or leftover files from previous executions from affecting new runs.

Changes Made

• Added a new method clear_output_dir() to StorageManager to delete and recreate the worker's output directory
• Called clear_output_dir() at the beginning of run_notebook() before syncing output

Related Issue

Fixes #333

Notes

• Manually tested using a custom .ipynb notebook file

[CLAassistant]

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