if (@ARGV == "clean"){ print "cleaning up dirs"; clean(); }
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@ARGV is a list of command-line parameters. What you probably want to do is check the first of these parameters:

if($ARGV[0] eq "clean") { # eq, not ==, for strings
  print "cleaning up dirs";
  clean();
}
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instead of comparing "the list".

A more advanced issue (feel free to skip this bit for now, while you get your code working) is that code like this (a huge chain of if..elsif...elsif...else) is likely to be difficult to maintain, if only because large blocks of code are daunting to mess with. Instead, I'd suggest building a dispatch table. First, write a bunch of handler functions, for instance:

sub clean_handler
{
  print "cleaning up dirs";
  clean();
}

sub make_handler
{
  print "making project";
  make();
}

# ...
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Next, build a hash of these handlers, keyed on the commands:

my %cmds = (
  'clean' => \&clean, # reference to the subroutine 'clean'
  'make'  => \&make,  # reference to 'make'
  # ...
);
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Now, when you get a command, retrieve the handler function from the %cmds hash and call it:

my $cmd = $cmds{$ARGV[0]}; # get the coderef
&$cmd();                   # call it
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