This UI reshuffling proposes to address the following issues:
Mockup

User role driven navigation
When new users logs into the system, they will typically look for a navigation bar on the left. However, what they look for will depend on their specific role.
For example, for workflow operators who are only interested in running pre-made workflows, the tool panel is of little relevance. Currently, such users will have to scan for their starting point, which is actually on the top menu bar under the “workflows” menu. They will have to click the workflows menu, click the dropdown to view the menu, and then finally click “run“, requiring at least 3 clicks before a desired workflow can be run. This can be reduced to a single click if the navigation panel shows the workflow tab straight away, which can be determined based on the user’s role/personalization settings.
Therefore, the proposed tabbed navigation layout allows for user specific tuning, where a workflow designer could have a different starting tab from a workflow operator, while still keeping the overall navigation design consistent for users who span multiple roles.
Tabbed navigation

The history and tool panels can be merged into a single, tabbed panel. This has the following advantages:

Unified search
A unified, always visible search bar has the following advantages

Disadvantages
Additional Notes
Would be great to hear feedback on the merits and demerits of this proposal.
@nuwang thanks for a nice proposal. My notes:
Unified tool/history panel is not a good idea. Often you need to see both and therefore history should be readily accessible at all times. In addition the history itself is a moving target - we are getting (hopefully) closer to having a graph-based history view. I think we really need developers to use Galaxy more in real world situations (not just the cut tool).
I do need to see the the tool form and the history at the same time, but the tool panel on the left and the history panel on the right I don't think I need to see at the same time and I can imagine that this could work out fine ?
@nuwang re:masthead, maybe moving the respective search inside of the tab would help that

We developed a long time ago a similar concept as a webhook. We called this overlay-search. We have chosen to go for a webhook to be optional and gather feedback for such a radical change.
https://github.com/galaxyproject/galaxy/tree/dev/config/plugins/webhooks/demo/search
What this is doing is a lot like what @nuwang proposes just as a webhook. You have a tab-based search, you can search for all the things in parallel and you can pin- tools/workflows, manage your favorites and so on.
One reason we went for a full-screen overlay search is to show more tools/workflows but also more metadata associated with an object.
Here is the PR https://github.com/galaxyproject/galaxy/pull/3460
There is a similar concept called Gnome-shell if people are interested in it: https://en.wikipedia.org/wiki/GNOME_Shell
I'm very much in favor of such change as findability is really not great in Galaxy at the moment.
I'd like to clarify that unified search was not the main goal. The goal was to collapse the tool and history panels into a tabbed view, for a number of benefits as outlined above. As @martenson proposed, this can be easily worked around by keeping individual search boxes as is. My own view of unified search is not to have global search results, but to have contextual search. That is, if the tool panel is active, only tools would be searched. If the history pane is active, that would be searched. Optionally, users could select multiple items to search (which would then make the search "unified"). However, to avoid this confusion, perhaps the proper term is "contextual search". All for the marginal benefit of saving some screen real-estate and providing a single constant search location, so it's not that important IMO.
@martenson
Making the masthead more than double the height is problematic. Top edge is the prime space of any webpage, it should be filled with the most important things.
I agree. It could partially be mitigated in combination with this: https://github.com/galaxyproject/galaxy/issues/9037
but the better option sounds like simply dropping the single search box as in your screenshot.
our 'standard' will never fit mobile without a significant investment.
True. The tabbed design better supports mobile as a pleasant side-effect, but overall, I agree that it need not be a concern. Tablets seemed to be used though.
Have you seen/tried the unified search webhook? Is it close to what you imagine?
I have seen this before, but as mentioned in the previous comment, was thinking more of a contextual search.
I'd be happy to give you access to the Main's analytics if you'd like.
It would be great to discuss this more. In a certain sense, perhaps this could be a low-cost opportunity to promote workflows more and drive adoption. But yes, I do agree with your concern.
@nekrut For users that need to see both, would the "pin" option not suffice?
Perhaps. As @mvdbeek noted it would be nice to see a prototype of some sort
i have a problem with search tool, is that the the searched tool not appear in the list