Change the default values for several options

* doc/org-manual.org (Execute commands in the active region):
Update the manual given the new defaults.

* etc/ORG-NEWS (New default settings for some options): New
section.

* lisp/org.el (org-loop-over-headlines-in-active-region):
Change the default value to `t'.
(org-fontify-done-headline): Ditto.

* lisp/org-agenda.el
(org-agenda-loop-over-headlines-in-active-region): Ditto.

* lisp/org-src.el (org-src-tab-acts-natively): Ditto.

doc/org-manual.org

@@ -18661,23 +18661,22 @@ settings[fn:148]:
 :END:
 
 #+vindex: org-loop-over-headlines-in-active-region
-When in an Org buffer, you might want to apply a command to all the
-subtrees in the active region.  To enable this, set the option
-~org-loop-over-headlines-in-active-region~ to non-~nil~, activate the
-region and run the command normally.  For example, hitting {{{kbd(C-c
-C-s)}}} when multiple headlines are within the active region will
-successively prompt you for a new schedule date and time.
+When in an Org buffer and the region is active, some commands will
+apply to all the subtrees in the active region.  For example, hitting
+{{{kbd(C-c C-s)}}} when multiple headlines are within the active region will
+successively prompt you for a new schedule date and time.  To disable
+this, set the option ~org-loop-over-headlines-in-active-region~ to
+non-~t~, activate the region and run the command normally.
 
 #+vindex: org-agenda-loop-over-headlines-in-active-region
-~org-agenda-loop-over-headlines-in-active-region~ lets you obtain the
-same behavior within an agenda buffer.  In the agenda, you can also
-use [[*Bulk remote editing selected entries][bulk editing of selected entries]], which see.
+~org-agenda-loop-over-headlines-in-active-region~ is the equivalent
+option of the agenda buffer, where you can also use [[*Bulk remote editing selected entries][bulk editing of
+selected entries]].
 
 Not all commands can loop in the active region and what subtrees or
 headlines are considered can be refined: see the docstrings of these
 options for more details.
 
-
 ** Dynamic Headline Numbering
 :PROPERTIES:
 :DESCRIPTION: Display and update outline numbering.

etc/ORG-NEWS

@@ -44,15 +44,28 @@ resulting <div> will be ~<div id="outline-container-my-headline">~.
 You may want to check whether your HTML files are rendered differently
 after this change.
 
+** New default settings for some options
+
+These options now defaults to =t=:
+
+- ~org-loop-over-headlines-in-active-region~
+- ~org-fontify-done-headline~
+- ~org-src-tab-acts-natively~
+
+You may want to read the docstrings of these options to understand the
+consequences of this change.
+
 ** New features
 
 *** Looping agenda commands over headlines
 
 ~org-agenda-loop-over-headlines-in-active-region~ allows you to loop
-agenda commands over the active region.  When set to =t=, loop over
-all headlines.  When set to ='start-level=, loop over headlines with
-the same level than the first headline in the region.  When set to a
-string, loop over lines matching this regular expression.
+agenda commands over the active region.
+
+When set to =t= (the default), loop over all headlines.  When set to
+='start-level=, loop over headlines with the same level than the first
+headline in the region.  When set to a string, loop over lines
+matching this regular expression.
 
 *** New minor mode ~org-table-header-line-mode~
 

lisp/org-agenda.el

@@ -10284,7 +10284,7 @@ bulk action."
   :version "24.1"
   :type 'boolean)
 
-(defcustom org-agenda-loop-over-headlines-in-active-region nil
+(defcustom org-agenda-loop-over-headlines-in-active-region t
   "Shall some commands act upon headlines in the active region?
 
 When set to t, some commands will be performed in all headlines
@@ -10307,6 +10307,7 @@ option for Org buffers."
 		 (const :tag "All headlines in active region" t)
 		 (const :tag "In active region, headlines at the same level than the first one" start-level)
 		 (regexp :tag "Regular expression matcher"))
+  :version "27.1"
   :package-version '(Org . "9.4")
   :group 'org-agenda)
 

lisp/org-src.el

@@ -237,11 +237,12 @@ green, respectability.
   :version "26.1"
   :package-version '(Org . "9.0"))
 
-(defcustom org-src-tab-acts-natively nil
+(defcustom org-src-tab-acts-natively t
   "If non-nil, the effect of TAB in a code block is as if it were
 issued in the language major mode buffer."
   :type 'boolean
-  :version "24.1"
+  :version "27.1"
+  :package-version "9.4"
   :group 'org-babel)
 
 

lisp/org.el

@@ -893,7 +893,7 @@ will still edit the time stamp - this is just too good to give up."
 	  (const :tag "When outside special context" t)
 	  (const :tag "Everywhere except timestamps" always)))
 
-(defcustom org-loop-over-headlines-in-active-region nil
+(defcustom org-loop-over-headlines-in-active-region t
   "Shall some commands act upon headlines in the active region?
 
 When set to t, some commands will be performed in all headlines
@@ -919,7 +919,8 @@ equivalent option for agenda views."
 		 (const :tag "All headlines in active region" t)
 		 (const :tag "In active region, headlines at the same level than the first one" start-level)
 		 (string :tag "Tags/Property/Todo matcher"))
-  :version "24.1"
+  :version "27.1"
+  :package-version "9.4"
   :group 'org-todo
   :group 'org-archive)
 
@@ -3531,12 +3532,14 @@ When this is non-nil, the headline after the keyword is set to the
   :type 'boolean
   :safe t)
 
-(defcustom org-fontify-done-headline nil
+(defcustom org-fontify-done-headline t
   "Non-nil means change the face of a headline if it is marked DONE.
 Normally, only the TODO/DONE keyword indicates the state of a headline.
 When this is non-nil, the headline after the keyword is set to the
 `org-headline-done' as an additional indication."
   :group 'org-appearance
+  :version "27.1"
+  :package-version "9.4"
   :type 'boolean)
 
 (defcustom org-fontify-emphasized-text t