gistfile1.txt

#!/bin/bash
# vim:ft=sh:ts=3:sts=3:sw=3:et:

###
# Strips the closing php tag `?>` and any following blank lines from the
# end of any PHP file in the current working directory and sub-directories. Files
# with non-whitespace characters following the closing tag will not be affected.
#
# Author: Bryan C. Geraghty <bryan@ravensight.org>
# Date: 2009-10-28
##

if [ -z "$1" ]; then
	echo "No path given, script usage: ./clean.sh <path>";
	exit 1;
fi

FILES=$(find $1 -name '*.php');

for FILE in $FILES;
do
	MATCH=`pcregrep -rnM  '^(\n|\?\>)(?=([\s\n]+)?$(?!\n))' $FILE`
	if [ "$MATCH" != "" ]; then
		TARGET=`echo $MATCH | awk -F ':' '{print $1}'`;
		LINE_COUNT=`wc -l $FILE | awk -F " " '{print $1}'`;
		echo "Removing lines ${TARGET} through ${LINE_COUNT} from file $FILE...";
		sed -i '' "${TARGET},${LINE_COUNT}d" $FILE;
	fi
done;

Or on shell in one command (this was typo3 cms, #52360):

find . -type d ( -path ./typo3/contrib/idna -o -path ./typo3/contrib/pear -o -path ./typo3/sysext/adodb/adodb -o -path ./typo3/sysext/openid/lib/php-openid -o -path ./typo3/sysext/openid/lib/php-openid/Auth ) -prune -o -name '*.php' -print | while read FILE; do tail -n1 $FILE | grep '^?>$' && sed -i '$ d' $FILE; done

tweaked it a bit to remove empty newlines on the end too

@lolli42: thanks ;) Too bad that one didn't turn up in my google search ;)