This is the official manual for the latest Org-mode release.

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15.10.2 Packages that conflict with Org mode

In Emacs, shift-selection-mode combines cursor motions with shift key to enlarge regions. Emacs sets this mode by default. This conflicts with Org's use of S-<cursor> commands to change timestamps, TODO keywords, priorities, and item bullet types, etc. Since S-<cursor> commands outside of specific contexts don't do anything, Org offers the variable org-support-shift-select for customization. Org mode accommodates shift selection by (i) making it available outside of the special contexts where special commands apply, and (ii) extending an existing active region even if the cursor moves across a special context.
CUA.el by Kim. F. Storm
Org key bindings conflict with S-<cursor> keys used by CUA mode. For Org to relinquish these bindings to CUA mode, configure the variable org-replace-disputed-keys. When set, Org moves the following key bindings in Org files, and in the agenda buffer (but not during date selection).
          S-UP      ⇒  M-p             S-DOWN     ⇒  M-n
          S-LEFT    ⇒  M--             S-RIGHT    ⇒  M-+
          C-S-LEFT  ⇒  M-S--           C-S-RIGHT  ⇒  M-S-+

Yes, these are unfortunately more difficult to remember. To define a different replacement keys, look at the variable org-disputed-keys.

ecomplete.el by Lars Magne Ingebrigtsen
Ecomplete provides “electric” address completion in address header lines in message buffers. Sadly Orgtbl mode cuts ecompletes power supply: No completion happens when Orgtbl mode is enabled in message buffers while entering text in address header lines. If one wants to use ecomplete one should not follow the advice to automagically turn on Orgtbl mode in message buffers (see Orgtbl mode), but instead—after filling in the message headers—turn on Orgtbl mode manually when needed in the messages body.
filladapt.el by Kyle Jones
Org mode tries to do the right thing when filling paragraphs, list items and other elements. Many users reported problems using both filladapt.el and Org mode, so a safe thing to do is to disable filladapt like this:
          (add-hook 'org-mode-hook 'turn-off-filladapt-mode)

The way Org mode binds the <TAB> key (binding to [tab] instead of "\t") overrules YASnippet's access to this key. The following code fixed this problem:
          (add-hook 'org-mode-hook
                    (lambda ()
                      (org-set-local 'yas/trigger-key [tab])
                      (define-key yas/keymap [tab] 'yas/next-field-or-maybe-expand)))

The latest version of yasnippet doesn't play well with Org mode. If the above code does not fix the conflict, first define the following function:

          (defun yas/org-very-safe-expand ()
            (let ((yas/fallback-behavior 'return-nil)) (yas/expand)))

Then tell Org mode to use that function:

          (add-hook 'org-mode-hook
                    (lambda ()
                      (make-variable-buffer-local 'yas/trigger-key)
                      (setq yas/trigger-key [tab])
                      (add-to-list 'org-tab-first-hook 'yas/org-very-safe-expand)
                      (define-key yas/keymap [tab] 'yas/next-field)))

windmove.el by Hovav Shacham
This package also uses the S-<cursor> keys, so everything written in the paragraph above about CUA mode also applies here. If you want make the windmove function active in locations where Org mode does not have special functionality on S-<cursor>, add this to your configuration:
          ;; Make windmove work in org-mode:
          (add-hook 'org-shiftup-final-hook 'windmove-up)
          (add-hook 'org-shiftleft-final-hook 'windmove-left)
          (add-hook 'org-shiftdown-final-hook 'windmove-down)
          (add-hook 'org-shiftright-final-hook 'windmove-right)

viper.el by Michael Kifer
Viper uses C-c / and therefore makes this key not access the corresponding Org mode command org-sparse-tree. You need to find another key for this command, or override the key in viper-vi-global-user-map with
          (define-key viper-vi-global-user-map "C-c /" 'org-sparse-tree)