Eclipse Photon perspectives behave differently from Eclipse Mars (= weird)

Question

I've been using PyDev with Eclipse Mars for a long time, with basically a pydev and a debug perspective. Both showed different layout and views, but they were synchronized in the sense that when I loaded another source file into the pydev perspective, it would also show up in the debug perspective, along with the already loaded source files.

After upgrading to Eclipse Photon (Rust as I might want to try that, no errors/warnings when adding PyDev), the perspectives are a mess. Every time Eclipse starts, it adds a second "Debug" perspective. A second Console view is added when running a program although there is one already. Non-source views like Variables, Search, Tasks pop up in both perspectives and when I remove them from one, they're gone in the other perspective as well. In effect, I cannot define two separate perspectives for the two tasks anymore.

I feel I do not understand the UI hierarchy: There is a window, and there are views, but views are grouped inside a window into "panels", for which I do not find terminology or functions to organize them.

What has changed in terms of perspective handling between Mars and Photon?

EDIT: There seem to be two kinds of "panels": Some predefined panels do not disappear when I remove the last view in them (empty tab bar and white content area), while other panels (which I created by dragging a view to a border location) disappear when I remove the last view in them...

To Till's comment, there are a few errors when starting Eclipse (I cleared the log after changing to a fresh workspace, and have removed the call stack):

!ENTRY org.eclipse.ui 2 2 2018-07-29 14:50:21.855 
!MESSAGE Invalid property category path: org.eclipse.cdt.managedbuilder.ui.properties.Page_head_build (bundle: org.eclipse.cdt.ui, propertyPage: org.eclipse.cdt.managedbuilder.ui.properties.BuildLogPreferencePage) 
!SESSION 2018-07-29 14:50:26.758
----------------------------------------------- eclipse.buildId=4.8.0.I20180611-0500 java.version=1.8.0_92 java.vendor=Oracle Corporation BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=de_DE Framework arguments:  -product org.eclipse.epp.package.rust.product Command-line arguments:  -os win32 -ws win32 -arch x86_64 -product org.eclipse.epp.package.rust.product

!ENTRY org.eclipse.egit.core 2 0 2018-07-29 14:50:30.508 
!MESSAGE Builtin LFS support not present/detected !STACK 0 java.lang.ClassNotFoundException: org.eclipse.jgit.lfs.BuiltinLFS cannot be found by org.eclipse.egit.core_5.0.0.201806131550-r 
:
:


!ENTRY org.eclipse.launchbar.core 2 0 2018-07-29 14:50:37.600 
!MESSAGE Enablement expression is missing for descriptor type org.eclipse.cdt.debug.core.coreBuildDescriptorType

!ENTRY org.eclipse.launchbar.core 2 0 2018-07-29 14:50:37.772 
!MESSAGE Enablement expression is missing for config provider for org.eclipse.cdt.debug.core.coreBuildDescriptorType

!ENTRY org.eclipse.launchbar.core 2 0 2018-07-29 14:50:37.881 
!MESSAGE Enablement expression is missing for config provider for org.eclipse.cdt.debug.core.coreBuildDescriptorType

!ENTRY org.eclipse.egit.ui 2 0 2018-07-29 14:50:38.287 
!MESSAGE Warning: The environment variable HOME is not set. The following directory will be used to store the Git user global configuration and to define the default location to store repositories: 'C:\Users\nobi'. If this is not correct please set the HOME environment variable and restart Eclipse. Otherwise Git for Windows and EGit might behave differently since they see different configuration options. This warning can be switched off on the Team > Git > Confirmations and Warnings preference page.

Answer 1

I don't think anything changed regarding perspectives...

I think what's happening is that Eclipse somehow became confused with your existing perspective in the workspace.

Note: a perspective is defined as a given organization of views, windows and active actions, and you should be free to close and open/customize perspectives as you wish.

My suggestion is closing the perspective(s) you don't want and then opening a new one to be fresh (you can close the perspective by using Ctrl+3, close perspective or right-clicking the perspective icon on the top-right corner... to create a new one, you can use the menu window > perspective > open perspective).

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Edit:

I think there may be a confusion of what's a perspective/view/contents inside view.

A perspective is mostly defining where views are located and the actions active in that given perspective.

A view on the other way is the same across the many different perspectives, so, changing the contents of a view will change its contents in all perspectives.