The following shell command uses the find function to find all files in or below the current directory that have the extension php. It then passes each file found onto a sed command which then replaces all with the longer <?php version.
find . -name '*.php' -exec sed -ie 's##The -name argument in find will look at the base of the file name, that is, the file without any directory path. The -exec command is used to pass each file found onto another command, in this case sed is used.