I'll focus on the main tab area (common functions) to keep things simple...
- chrome window icon is actually chromium?
- '-' and '+' is too small/micro
Also, the hierarchical lines are not really needed because you have nice indentation... reduce the clutter!
- I didn't realise the edge of the 'button tag' is also a button. It is also a very useful button once you find it. It allows for collapsing a root node in a tree. It is also a toggle so it's visual state should also update (which it doesn't). I suggest sticking to the '-+' concept in this case as it is a 1:1 version of clicking the same icon on the far left.
Further, the placement is inconsistent. You are hiding button options depending on the state of various tabs/nodes. This slows down the user experience because you have to move the mouse left and right. A better solution would be to use a disabled button state and therefore keep consistent layout and spacing of the interactive elements.
- A green cross is simply confusing. We are programmed to see a cross as delete and green to mean something good/safe. My brain has a micro flip out when I have to click that thing. It is hard to find something that fits though. I just played with it more and really what happens is the step before deleting that I would call "Disabled". So one disables and then deletes. Considering you no longer show the green X when a tab/window is disabled, why not simply leverage the trash icon better. The first click of the (gray) trash icon is to disable. The second click (on the now red trash icon) is to delete. This is common in iOS (2 step delete process). You don't have to avoid accidental deletions because you have 2 steps.
An alternative might be to replace the green X with a checkbox. Checkboxes signal on/off states which is also a good fit.
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