Confused about .emacs vs .emacs.d/init.el

Question

I read somewhere the two files were interchangeable, so I cut/paste the content of the former, shown below, to the latter. But then Xreader was missing when I tried to view a document generated by AUCTEX, which tells me they are not interchangeable.

 (custom-set-variables  ;; custom-set-variables was added by Custom. 
 ;; If you edit it by hand, you could mess it up, so be careful.  ;;
 Your init file should contain only one such instance.  ;; If there is
 more than one, they won't work right.  '(TeX-view-program-list (quote
 (("Xreader" ("xreader %o") "xreader"))))  '(TeX-view-program-selection
 (quote
     (((output-dvi has-no-display-manager)
       "dvi2tty")
      ((output-dvi style-pstricks)
       "dvips and gv")
      (output-dvi "xdvi")
      (output-pdf "Xreader")
      (output-html "xdg-open"))))) (custom-set-faces  ;; custom-set-faces was added by Custom.  ;; If you edit it by hand, you
 could mess it up, so be careful.  ;; Your init file should contain
 only one such instance.  ;; If there is more than one, they won't work
 right.  ) (put 'upcase-region 'disabled nil)

What are the different purposes of .emacs and .emacs.d/init.el?

UPDATE:

Here's the content of .emacs.d/init.el after the modification discussed above:

(require 'package)
(add-to-list 'package-archives '("org" . "https://orgmode.org/elpa/") t)
(require 'org)
(define-key global-map "\C-cl" 'org-store-link)
(define-key global-map "\C-ca" 'org-agenda)
(setq org-log-done t)
(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(TeX-view-program-list (quote (("Xreader" ("xreader %o") "xreader"))))
 '(TeX-view-program-selection
   (quote
    (((output-dvi has-no-display-manager)
      "dvi2tty")
     ((output-dvi style-pstricks)
      "dvips and gv")
     (output-dvi "xdvi")
     (output-pdf "Xreader")
     (output-html "xdg-open")))))
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 )
(put 'upcase-region 'disabled nil)

Answer 1

.emacs.d

A folder containing emacs config files.

Located at ~/.emacs.d/

---

.emacs

An init/config file with personal EmacsLisp code used to configure emacs when it starts up.

Usually located at ~/.emacs, ~/.emacs.el, or ~/.emacs.d/init.el.

---

init.el

Defaulted to by emacs during startup when the other .emacs and .emacs.el are both not available.

Usually located at ~/.emacs.d/init.el

---

custom set variables

(This is a response to a question asked about storing your custom-set-variables in some place other than the .emacs file)

Q: Can you store custom-set-variables in a place other than .emacs?
A: Yes

Many people do this by having their custom-set-variables inside their own file (lots of times called custom.el)
This is done by adding the following code into your main init file:

(setq custom-file (expand-file-name "custom.el" user-emacs-directory))
(load custom-file)

Which will now load your custom-set-variables and custom-set-faces from the file located in ~/.emacs.d/custom.el

Now inside your custom.el file (located in ~/.emacs.d/custom.el) you can have your custom-set-variables and custom-set-faces code.

---

on moving code from .emacs and init.el

I would be careful about where you put stuff and where emacs puts stuff, as sometimes they may not be the same place.

For example:

At one point I was adding config stuff in custom variables/custom themes that was in my .emacs file. I was loading a .org file into my .emacs file with extra config as well. But whenever I would evaluate my .emacs, the changes I made in the custom variables/custom themes weren't showing up all the time. Little did I know that the custom themes and custom variables that I was editing in my .emacs where not being evaluated by emacs at all and it was a completely different version that was getting evaluated which was located in my init.el file. So the only variables that would get loaded whenver I evaluated emacs where ones that I had set in emacs customize groups which were then getting placed in the init.el file and evaluated while what I was adding into the .emacs was being ignored.

To make a long story short: Be sure you know what emacs is really evaluating and what it isn't.