Note that the following answer is mostly a citation of two answers in the corresponding reddit article.
They changed the template system in orgmode 9.2.
You get the old easy-template system back
by adding (require 'org-tempo) to your init file or
by adding org-tempo to the list org-modules. You can do that by customizing org-modules.
Alternatively you ...
It's talking about the specific version of the package.
Let's look at the first D line there: avy. It's saying "avy version 20171230.220 is to be deleted".
Elsewhere in the buffer, you should see a later version of avy, with I next to it to mark the installation. Having both means the package will be upgraded.
In fact, Emacs will let you know that. When ...
Testing confirms that packages labeled "dependency" are those which are installed only because they are dependencies of other packages you have installed.
The package manager actually won't let you uninstall a dependency (as doing so would break the package that requires it). Similarly, uninstalling an "installed" package which is also a dependency of ...
I can't tell you what it means (I can guess, but you'll probably get a good answer here).
But I can tell you how to ask Emacs about it, in case you don't already know. Usually the Emacs doc provides such info (it should).
C-h f list-packages gives you a brief description of the command.
C-h r puts you in the Emacs manual. There, i list-packages takes you ...
Short answer: You should recompile Emacs.
When it is compiled, the emacs executable is dumped with numerous elisp libraries pre-loaded. Amongst these libraries is the loaddefs.el library containing the autoload declarations for autoloaded functions in the standard distribution.
So (a) deleting the libraries you don't want does not delete the ...
The elpa-version darkroom-0.1.el of darkroom does not have an ;;;###autoload before (define-minor-mode darkroom-mode ...) as the github version has.
That means that you can either install the the github version or put
(autoload 'darkroom-mode "darkroom" nil t)
into your init file.
To address the side questions:
Did I install Org 9.2 correctly?
Yes. Installing org via list-packages will "override" the default version. This can be seen by running org-version. Note that it may be necessary to restart Emacs (or the Emacs server).
If this is a bug, how do I submit it? With report-emacs-bug?
According to the org-mode homepage (at the ...
The documentation about package.el should be improved (see bug #29420). I think list-packages does not list all packages available on the system but only displays manageable packages (c.f. the built-in documentation).
The idea behind package.el is to be able to download packages and install them. Packages are versioned and have versioned dependencies....
I also tried to find a way to identify all packages in a way similar to list-packages, but it seems not all libraries are considered as packages so they are not listed among other packages.
There are a few ways of identify what is built-in into Emacs:
Official Manuals which cover a lot of things, including manuals for various packages including RCIRC: GNU ...
I can't help with what shows up when you do M+x package-list-packages, but to clean-up the command namespace (minibuffer prompt, functions available to you in lisp, etc) there are a few hacks.
You might be seeing functions even after deletion due to residual autoload files. Firstly you need to find out what are the locations of the ...
A quick stab at an answer. Someone may provide better info.
Sounds like package-list-packages lists as "built-in" those libraries that Emacs knows it builds in. And it sounds like that is the only indication you are seeing that they exist. Unless you find some other indication, you can probably assume that package-list-packages doesn't intend that "built-in"...
Regarding 'dependency', I believe this refers to a package that is required by another package. From the manual, (emacs) Package Installation.
A package may “require” certain other packages to be installed,
because it relies on functionality provided by them. When Emacs
installs such a package, it also automatically downloads and installs