i had also encountered this issue.
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This Solution worked for me....
windows->navigation->maximize active View or Editor(ctrl + M)
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in the screen you can see on left side navigation menus ... now click on those buttons one by one ....you will get your solution...
Not sure if this is problem but, this ticked me off for a while since I did not realize what was happening at first - maybe this will help others.
Its not really a problem, just the way Eclipse works. (I'm use to Visual studio)
Its all about Perspectives!
I set up an (existing) PHP project in eclipse(neon) and then tried to configure and run debug. A Popup "Confirm Perspective Switch" is shown - I selected "Yes", not realizing what it actually does. The "perspective" then changes and you no longer see the project explorer anywhere. You cant "open" the project explorer window from top nav > window > show view, since its no longer there (which is BS, it should show something that gives you indication of current and other "perspectives" - at least for newbie.) No where now does it give project explore options.
Now you must change the "perspective" back from debug to PHP (at least in in my case).
This can be done a couple ways, easiest is from the icons on right top right side side. One icon would be the "bug", and next to it is the PHP icon. Just click the icon "perspective" you want. The other way is from top nav bar > window > Perspective > open Perspective, then select PHP. Could they hide this any deeper?
I know this is likely second nature to those who have used eclipse for a while, but was frustrating to me (on day one) till I figured out what was going on.
If you are on either Eclipse or Spring tool suite then follow the below steps.
(1) Go to 'Window' on the top of the editor. Click on it
(2) Select show view. You should see an option 'Project Explorer'. Click on it.
You should be able to do it.