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#<?#<?php#' {} \;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.
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A quick note: if you are searching to replace a link to a directory ie text/documents to text/document/new you must escape the / char so for the above example the command would be:
find . -name '*.php' -exec sed -ie 's#text//documents#text//document//new#' {} \;