We assign tools a certain level of importance. Tools with high importance get their own dedicated space. Tools with low importance share space with other tools. For example, X-Ray and MRI machines are tools with very high importance, so they get their own space. We devote entire rooms to these tools. On the other hand, tongue depressor sticks, while still very useful, are lower importance. They typically share counter space with other low-import tools such as cotton swabs and tissues. This same rule also generally applies to virtual spaces, such as your desktop.
Important tools, such as your IDE, typically get their own space. Generally they at least get their own application window, sometimes you will even devote an entire desktop to them. Terminals and web browsers typically are the same way. This is not an accident. These tools are useful enough to have dedicated space. We spend enough time in them that it makes sense to give them dedicated space. We keep these tools clean and uncluttered. Imagine if you had pop-up adds showing up all the time when you were trying to write some code. Would you be able to focus if your IDE allowed that?
Other tools, such as your to-do list and calendar are typically less important than your IDE. These may still get their own application windows, but they are delegated to running in the background, perhaps on hidden desktops, and only show up when you summon them. Of course these are still tools that you need, but you do not need them to be prominent all the time.
Low importance tools share space with other tools. This manifests most often in the form of browser tabs. You need to look up the Javadocs for Date/Time formatting, so you open a new browser tab and search for that, leaving it open while you switch back to your IDE and fix the bug, switch back to your browser to find a screenshot in the JIRA ticket, then over to another tab to look at your locally running instance, etc. This becomes a dumping ground, where everything from reference information to your active tasks are being held.
Sometimes we make the mistake of trying to put important tools in a browser tab. Timers, to-do lists, even e-mail applications are fairly high-importance tools that we tend to pile into browser tabs. You may be able to get away with this perfectly fine, and there are tricks you can play to make this work, such as having a separate browser window open that is just for your e-mail application. You may be able to put off all your e-mails until a set time every day (this is a good idea any way). It takes you much longer to find that one essential thing when your browser is cluttered with tabs. Just like when your desk is piled high with clutter.
Be thoughtful about where you are putting your tools. We tend to gravitate towards websites in our browser tabs rather than installing applications for many things. Perhaps these tools would better serve you if they had dedicated space. Some may serve you even better if they had dedicated physical space on your desk.