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I have the following script working Emacs Auto Indent Mode

it does auto indenting but it has one problem when i start marking regions and go down by lines each time i hit the indention the marking is canceled and it kind-of annoyance me.

How can this be fixed or are there any alternatives? or how can i disable auto indention when marking region is active

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It sounds like you have Transient Mark mode enabled. Try putting this at the bottom or your ~/.emacs file:

;; Turn off Transient Mark mode.
(transient-mark-mode -1)

and restart Emacs.

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