Here is what I came up with after a quick run through at your request:

#!/usr/bin/perl -w
=head Changes
Be more consistant with your spacing.
I don't see the use for which() since you are just duplicating code th
+at
    the kernel will do but less portably (under Win32, you need to spl
+it
    on ';', not on ':').
Used a more "standard" method for picking an editor.
Since you only have one enclosing loop, you don't need the STUDY: labe
+l,
    but I don't mind you keeping it since it makes it easy to find tha
+t loop.
On non-Unix systems, $ENV{HOME} may not be set.
Declaring subs in the middle of code just makes them hard to find.
Added a default for $ENV{SANDBOX}
s/[A-Za-z]/0/g more efficient as tr/A-Za-z/0/
Allow easy highlight with a color other than 'GREEN'
Replace repeated highlighting code with a subroutine
Treat $hide_help and $clear as Booleans instead of integers
Your first "next" doesn't do anything (I just commented it out)
Your first "redo" doesn't do anything (commented out)
Don't have a [my] variable with the same name as a global, STUDYPATH
close SCRIPT when you are done with it
=cut

use strict;

use Term::ANSIColor 'color';

my $EDITOR    = $ENV{VISUAL} || $ENV{EDITOR} || $ENV{EDIT}
                    or  $^O =~ /^MSWin/ ? 'notepad' : 'vi';
my $index     = @ARGV ? shift(@ARGV) :0;
my $clear     = 1;
my $hide_help = 0;
my $highlight = $ENV{STUDYCOLOR} || 'GREEN';

my $homedir   = $ENV{HOME} || '.';
my $sandbox   = $ENV{SANDBOX} || 'sandbox';
my $STUDYPATH = "$homedir/$sandbox";

sub change_snippet_dir{
    my $sandbox= shift;
    my $path= "$homedir/$sandbox";
    if(  -d $path  ) {
        $STUDYPATH= $path;
    }
}

sub highlight {
    return color($highlight), @_, color('reset');
}

STUDY:
while (1) {
    my @files= glob "$STUDYPATH/*";
    if( $clear ) {
        system ('clear');
    } else {
        $clear++;
    }
    $index =~ tr/A-Za-z/0/;
    $index= 0   if  $index < (0-$#files)-1  ||  $index > $#files;
    printf( "%50s <- (%5s)\n", $files[$index], $index );
    print "
    ",highlight("[C]"),"HANGE editor. Currently $EDITOR
    ",highlight("[E]"),"DIT to open the snippet in an editor
    ",highlight("[G]"),"oTo to select file index: -", ($#files+1)," to
+ $#files
    ",highlight("[H]"),"ELP to (un)hide this menu
    ",highlight("[N]"),"EXT to skip this snippet
    ",highlight("[R]"),"EDO to revisit the previous snippet
    ",highlight("[Q]"),"UIT to exit
    e",highlight("[X]"),"ecute
    Any other key +",highlight(" [ENTER] "),"to print out the snippet
->      "
    unless $hide_help;

    my $input = <>;

    if ($input =~ /^N/i){
        ++$index;
        # next; This doesn't do anything

    }elsif($input =~ /^G/i){
        print "enter a number from -",$#files+1," to $#files
        ->   ";
        $index = <>;
        chomp $index;

    }elsif($input =~ /^H/i){
        $hide_help= ! $hide_help;

    }elsif($input =~ /^C/i){
        $EDITOR = <>;
        chomp $EDITOR;
        # redo STUDY;

    }elsif($input =~ /^R/i){
        --$index;

    }elsif($input =~ /^(SANDBOX)/i){
        print "$homedir/"; 
        my $sandbox=<>;
        chomp $sandbox;
        change_snippet_dir($sandbox);

    }elsif($input =~ /^E/i){
        system( $EDITOR, $files[$index] );

    }elsif($input =~ /^X/i){
        do $files[$index];
        print "\n";
        $clear= 0;

    }elsif($input =~ /^Q/i){
        last;

    }else{
        $clear= 0;
        open (SCRIPT,"< $files[$index]") 
                                or warn "can't open file: $!";
        print while <SCRIPT>;
        close SCRIPT;
    }
}
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