The left panel now feels a bit clattered with all the features together.

I think we need to keep the tree view on the top of the panel always and have two smaller "sub-panels" at the bottom one for notebooks and the other for repositories:
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Tree View
...
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Repos * Notebooks
... * ...
*
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The left panel now feels a bit clattered with all the features together.

I think we need to keep the tree view on the top of the panel always and have two smaller "sub-panels" at the bottom one for notebooks and the other for repositories: