Here are my "secret" functions for cleaning up a source code file (biased for C or C++).
;; Code Cleanup for Emacs V1.0
;; http://blog.modp.com/2008/11/handy-emacs-functions-for-code-cleanup.html
;; PUBLIC DOMAIN
;; zap tabs
;;
(defun buffer-untabify ()
"Untabify an entire buffer"
(interactive)
(untabify (point-min) (point-max)))
;;
;; re-indent buffer
;;
(defun buffer-indent()
"Reindent an entire buffer"
(interactive)
(indent-region (point-min) (point-max) nil))
;;
;; Untabify, re-indent, make EOL be '\n' not '\r\n'
;; and delete trailing whitespace
;;
(defun buffer-cleanup()
"Untabify and re-indent an entire buffer"
(interactive)
(if (equal buffer-file-coding-system 'undecided-unix )
nil
(set-buffer-file-coding-system 'undecided-unix))
(setq c-basic-offset 4
tab-width 4
indent-tabs-mode nil)
(buffer-untabify)
(buffer-indent)
(delete-trailing-whitespace))
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