List of steps to reproduce (step by step, including full links if applicable):

1. LocalSettings.php

$wgScriptPath = "";
$wgArticlePath = "/wiki/$1";
$wgActionPaths['view'] = $wgArticlePath;

2. visit main page (any page would work actually)

What happens?:
URL generated are not prettified, ex:

• Login: index.php?title=Special:UserLogin&returnto=MediaWiki
• Permanent link: index.php?title=MediaWiki&oldid=3878227
• Cite this page: index.php?title=Special:CiteThisPage&page=MediaWiki&id=3878227&wpFormIdentifier=titleform

What should have happened instead?:
URLs should be prettified ex:

• Login: /Special:UserLogin?returnto=MediaWiki
• Permanent link: /MediaWiki?oldid=3878227
• Cite this page: /Special:CiteThisPage?page=MediaWiki&id=3878227&wpFormIdentifier=titleform

Software version (if not a Wikimedia wiki), browser information, screenshots, other information, etc.:
MediaWiki 1.37.2 but the code seems to be the same on latest master
https://github.com/wikimedia/mediawiki/blob/master/includes/Title.php#L2277

From
https://phabricator.wikimedia.org/rMW7bbce3f6feded604919290c3825398b18ede9351#change-TW14alGcSnux

Suggested fix:
The issue is due to these urls doesn't have action=view (most view actions aren't included in the generated URL?)
We have tested the following change on our wiki instance with success.
However, a proper fix may be to update the regex to recognize that action may not always be provided when its view action?

diff --git a/includes/Title.php b/includes/Title.php
index 33f9d390c2..936d3abddb 100644
--- a/includes/Title.php
+++ b/includes/Title.php
@@ -2342,7 +2342,14 @@ class Title implements LinkTarget, PageIdentity, IDBAccessObject {
 					if ( $query == '-' ) {
 						$query = '';
 					}
-					$url = "{$wgScript}?title={$dbkey}&{$query}";
+					if ( isset( $articlePaths['view'] ) ) {
+						$url = str_replace( '$1', $dbkey, $articlePaths['view'] );
+						if ( $query != '' ) {
+							$url = wfAppendQuery( $url, $query );
+						}
+					} else {
+						$url = "{$wgScript}?title={$dbkey}&{$query}";
+					}
 				}
 			}
 			Hooks::runner()->onGetLocalURL__Internal( $this, $url, $query );