Fix bundle generate job to preserve nested notebook directory structure

[varundeepsaini]

Changes

Fixes #4503.

Add MarkTasksForDownload that computes a common base path across all notebook tasks before downloading, replacing the per-task loop in job.go. This preserves nested directory structure instead of flattening all notebooks into src/.

Tests

• Unit tests for commonDirPrefix and MarkTasksForDownload.
• Acceptance test bundle/generate/job_nested_notebooks reproducing the issue.
• No regressions in existing python_job, ipynb_job, git_job tests.

Test are written by Claude Code

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Inputs:

• PR number: 4596
• Commit SHA: dc572e1f4db03136d474c4e0a77f14496a318056

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