// find and replace all characters with nothing in files ending in .php
perl -pi -w -e 's/.//g;' *.php

// find and replace all line breaks with nothing in files ending in .php
perl -pi -w -e 's/\n//g;' *.php

// append contents of template.php to every file in directory
for f in *; do cat ../template.php >> "$f"; done

Find and replace contents of files ending in .php with nothing.  then append contents of template.php to all files in directory

Batch file content replace from template.php

Bash, unix, perl

Bash