While there are some occasions that using shell commands from Perl are justified, there are many more when they are not. Decide: use the shell OR use Perl. Mixing them is to encourage inefficiency.
This is a rough conversion table from UNIX commands to Perl. Please note that there are not always direct single equivalents, and that there are certainly many more that I can't think of (but many others will).

UNIX	Perl	Origin
.	do	built-in
awk	perl ;-) (often 'split')	built-in
basename	File::Basename::basename	Base module
cat	while(<>){print}	built-in
	ExtUtils::Command::cat	Base module
cd	chdir	built-in
chmod	chmod	built-in
chown	chown	built-in
cp	File::Copy	Base module
	ExtUtils::Command::cp	Base module
date	localtime	built-in
	POSIX::strftime	Base module
declare	see typedef
df	Filesys::Df	CPAN
diff	File::Compare	Base module
dirname	File::Basename::dirname	Base modules
echo	print	built-in
egrep	while(<>){print if /re/}	built-in
eval	eval	built-in
exec	exec	built-in
	pipe (co-processes)	built-in
	open (file descriptors)	built-in
export	Assign to %ENV	Hash variable
	Env::C	CPAN
find	File::Find	Base module
ftp	Net::Ftp	Base module
function	sub	built-in
grep	see egrep
integer	int	built-in
kill	kill	built-in
ln -s	link	built-in
ls	glob	built-in
	opendir/readdir/closedir	built-in
	stat/lstat	built-in
mkdir	mkdir	built-in
mkpath	ExtUtils::Command::mkpath	Base module
mv	rename	built-in
	ExtUtils::Command::mv	Base module
od	ord	built-in
	printf	built-in
print	print	built-in
printf	printf	built-in
rand	rand	built-in
rm	unlink	built-in
	ExtUtils::Command::rm	Base module
rm –f	ExtUtils::Command::rm_rf	Base module
sed	s/// (usually)	built-in
select	Shell::POSIX::select	CPAN
sleep	sleep	built-in
	alarm	built-in
sort	sort	built-in
source	do	built-in
tail	File::Tail	CPAN
times	times	built-in
touch	open()/close()	built-in
	ExtUtils::Command::touch	Base module
trap	%SIG	Hash
	sigtrap	pragma
typeset	my	built-in
typeset –i	int	built-in
typeset –l	lc	built-in
typeset –u	uc	built-in
typeset -Z	sprintf	built-in

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