After clean install of Leopard, unix file folders are visible in finder

I did a DoD wipe of my hdd in my Mac Mini.
I installed Leopard, no frills, and got it registered to me like when I bought it.
I wanted to check if all is will BUT in the root folder in Finder (Macintosh HD) it shows folders like BIN, VAR and so on.
I thought maybe I had hidden files shown on the finder so I checked, its not supposed to show hiden files. So I toggled it on, applied and then turned it off and applied again. They are not gone!
So I tried the terminal way with these commands
defaults write com.apple.finder AppleShowAllFiles FALE
killall Finder
I also did a Disk Utility repair permissions.
These did not fix the issue. I am looking on Google and this seems to be fairly common but I haven't found a fix yet. Any ideas? I don't MIND they are there, but I have my wife who is not savy with the Mac yet so I am fearful she might remove the folders on accident especially with organizing her files, I have seen it happen on a Windows Machine.

Try these:
*cd /Volumes/Mac\ OS\ X\ Install\ DVD/*
*open System/Installation/Packages/*
OPTION-click on the OSInstall.mpkg and select show package contents. Then, drill down to Resources and copy the "SetHidden" file to your home folder and the "hidden_MacOS9" file to the root level of your boot volume. Launch the Terminal app and run the command:
*sudo SetHidden / hidden_MacOS9*
and restart.

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    PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/libexec;clear;cd;p=(1248 ' 0.5 0.25 10 1000 15 5120 1000 25000 1 1 0 100 ' 51 25600 4 10 25 5120 102400 1000 25 1000 150 40 500 300 85 25 20480 262144 20 2000 524288 604800 5 );k=({Soft,Hard}ware Memory Diagnostics Power FireWire Thunderbolt USB Bluetooth SerialATA Extensions Applications Frameworks PrefPane Fonts Displays PCI UniversalAccess InstallHistory ConfigurationProfile AirPort 'com\.apple\.' -\\t N\\/A 'AES|atr|udit|msa|dnse|ax|ensh|fami|FileS|fing|ft[pw]|gedC|kdu|etS|is\.|alk|ODSA|otp|htt|pcas|ps-lp|rexe|rlo|rsh|smb|snm|teln|upd-[aw]|uuc|vix|webf' OSBundle{Require,AllowUserLoa}d 'Mb/s:per sec:ms/s:KiB/s:%:total:MB:total' 'Net in:Net out:I/O wait time:I/O requests:CPU usage:Open files:Memory:Mach ports:File opens:Forks:Failed forks:System errors' 'tsA|[ST]M[HL]' PlistBuddy{,' 2>&1'}' -c Print' 'Info\.plist' CFBundleIdentifier );f=('\n%s'{': ','\n\n'}'%s\n' '\nRAM details\n%s\n' %s{' ','\n'{"${k[22]}",}}'%s\n' '%d MB: %s\n' '\n    ...and %s more line(s)\n' '\nContents of %s\n    '"${k[22]}"'mod date: %s\n    '"${k[22]}"'checksum: %s\n%s\n' );c=(879294308 4071182229 461455494 3627668074 1083382502 1274181950 1855907737 2758863019 1848501757 464843899 2636415542 3694147963 1233118628 2456546649 2806998573 2778718105 842973933 2051385900 3301885676 891055588 998894468 695903914 1443423563 4136085286 3374894509 1051159591 892310726 1707497389 523110921 2883943871 3873345487 );s=(' s/[0-9A-Za-z._]+@[0-9A-Za-z.]+\.[0-9A-Za-z]{2,4}/EMAIL/g;/faceb/s/(at\.)[^.]+/\1NAME/g;/\/Shared/!s/(\/Users\/)[^ /]+/\1USER/g;s/[-0-9A-Fa-f]{22,}/UUID/g;' ' s/^ +//;/de: S|[nst]:/p;' ' {sub(/^ +/,"")};/er:/;/y:/&&$2<'${p[4]} ' s/:$//;3,6d;/[my].+:/d;s/^ {4}//;H;${ g;s/\n$//;/s: (E[^m]|[^EO])|x([^08]|02[^F]|8[^0])/p;} ' ' 5h;6{ H;g;/P/!p;} ' ' ($1~/^Cy/&&$3>'${p[9]}')||($1~/^Cond/&&$2!~/^N/) ' ' /:$/{ N;/:.+:/d;s/ *://;b0'$'\n'' };/^ *(V.+ [0N]|Man).+ /{ s/ 0x.... //;s/[()]//g;s/(.+: )(.+)/ (\2)/;H;};$b0'$'\n'' d;:0'$'\n'' 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' ' 1s/^/\'$'\n''/;/^ +(([MNPRSV]|De|Li).+|Bus): .|d: Y/d;s/:$//;$d;p;' ' BEGIN { RS=",";FS=":";} $1~"name" { gsub("\"","",$2);print $2;} ' '|grep -q e:/' '/[^ .]/p' '{ print $1}' ' /^ +N.+: [1-9]/ { i++;} END { if(i) print "system: "i;} ' ' NF { print "'{admin,user}' "$NF;exit;} ' ' /se.+ =/,/[\}]/!d;/[=\}]/!p ' ' 3,4d;/^ +D|Of|Fu| [0B]/d;s/^  |:$//g;$!H;${ x;/:/p;} ' ' BEGIN { FS=": ";} NR==1 { sub(":","");h="\n"$1"\n";} /:$/ { l=$1;next;} $1~"S"&&$2!~3 { getline;next;} /^ {6}I/ { i++;L[i]=l" "$2;if(i=='${p[24]}') nextfile;} END { if(i) print h;for(j=0;j<i;j++) print L[i-j];} ' ' /./H;${ x;s/\n//;s/\n/, /g;/,/p;} ' );c1=(system_profiler pmset\ -g nvram fdesetup find syslog df vm_stat sar ps crontab kextfind top pkgutil "${k[30]}\\" echo cksum kextstat launchctl smcDiagnose sysctl\ -n defaults\ read stat lsbom 'mdfind -onlyin' env pluginkit scutil 'dtrace -q -x aggsortrev -n' security sed\ -En awk 'dscl . -read' networksetup mdutil lsof test osascript\ -e netstat mdls route cat );c2=(${k[21]}loginwindow\ LoginHook ' /L*/P*/loginw*' "'tell app \"System Events\" to get properties of login items'" 'L*/Ca*/'${k[21]}'Saf*/E* -d 2 -name '${k[32]} '~ $TMPDIR.. \( -flags +sappnd,schg,uappnd,uchg -o ! -user $UID -o ! -perm -600 \)' -i '-nl -print' '-F \$Sender -k Level Nle 3 -k Facility Req "'${k[21]}'('{'bird|.*i?clou','lsu|sha'}')"' "-f'%N: %l' Desktop {/,}L*/Keyc*" therm sysload boot-args status " -F '\$Time \$Message' -k Sender kernel -k Message CRne '0xdc008012|(allow|call)ing|(mplet|nabl)ed|ry HD|safe b|xpm' -k Message CReq 'bad |Can.t l|corru|dead|fail|GPU |hfs: Ru|inval|Limiti|v_c|NVDA[(]|pagin|Purg(ed|in)|error|Refus|TCON|tim(ed? ?|ing )o|trig|WARN' " '-du -n DEV -n EDEV 1 10' 'acrx -o%cpu,comm,ruid' "' syscall::recvfrom:return {@a[execname,uid]=sum(arg0)} syscall::sendto:return {@b[execname,uid]=sum(arg0)} syscall::open*:entry {@c[execname,uid,copyinstr(arg0),errno]=count()} syscall::execve:return, syscall::posix_spawn:return {@d[execname,uid,ppid]=count()} syscall::fork:return, syscall::vfork:return, syscall::posix_spawn:return /arg0<0/ {@e[execname,uid,arg0]=count()} syscall:::return /errno!=0/ {@f[execname,uid,errno]=count()} io:::wait-start {self->t=timestamp} io:::wait-done /self->t/ { this->T=timestamp - self->t;@g[execname,uid]=sum(this->T);self->t=0;} io:::start {@h[execname,uid]=sum(args[0]->b_bcount)} tick-10sec { normalize(@a,2560000);normalize(@b,2560000);normalize(@c,10);normalize(@d,10);normalize(@e,10);normalize(@f,10);normalize(@g,10000000);normalize(@h,10240);printa(\"1:%@d:%s:%d\n\",@a);printa(\"2:%@d:%s:%d\n\",@b);printa(\"9:%@d:%s:%d:%s:%d\n\",@c);printa(\"10:%@d:%s:%d:%d\n\",@d);printa(\"11:%@d:%s:%d:%d\n\",@e);printa(\"12:%@d:%s:%d:%d\n\",@f);printa(\"3:%@d:%s:%d\n\",@g);printa(\"4:%@d:%s:%d\n\",@h);exit(0);} '" '-f -pfc /var/db/r*/'${k[21]}'*.{BS,Bas,Es,J,OSXU,Rem,up}*.bom' '{/,}L*/Lo*/Diag* -type f -regex .\*[cght] ! -name .?\* ! -name \*ag \( -exec grep -lq "^Thread c" {} \; -exec printf \* \; -o -true \) -execdir stat -f:%Sc:%N -t%F {} \;' '/S*/*/Ca*/*xpc*' '-L /{S*/,}L*/StartupItems -type f -exec file {} +' /\ kMDItemContentTypeTree=${k[21]}{bundle,mach-o-dylib} :Label "/p*/e*/{aut*,{cron,fs}tab,hosts,{[lp],sy}*.conf,mach_i*/*,pam.d/*,ssh{,d}_config,*.local} {/p*,/usr/local}/e*/periodic/*/* /L*/P*{,/*}/com.a*.{Bo,sec*.ap}*t {/S*/,/,}L*/{Lau,Sec}*/*t .launchd.conf" list '-F "" -k Sender hidd -k Nle 3' /Library/Preferences/${k[21]}alf\ globalstate --proxy '-n get default' print\ system --dns -get{dnsservers,info} dump-trust-settings\ {-s,-d,} -n1 '-R -ce -l1 -n5 -o'{'prt -stats prt','mem -stats mem'}',command,uid' -kl -l -s\ / '--regexp --files '${k[21]}'pkg.*' '+c0 -i4TCP:0-1023' ${k[21]}dashboard\ layer-gadgets '-d /L*/Mana*/$USER' '-app Safari WebKitDNSPrefetchingEnabled' '-Fcu +c0 -l' -m 'L*/{Con*/*/Data/L*/,}Pref* -type f -size 0c -name *.plist.???????' kern.memorystatus_vm_pressure_level '3>&1 >&- 2>&3' '-F \$Message -k Sender kernel -k Message CReq "'{'n Cause: -','(a und|I/O |jnl_io.+)err','USBF:.+bus'}'"' -name\ kMDItem${k[33]} -T\ hfs '-n get default' -listnetworkserviceorder :${k[33]} :CFBundleDisplayName $EUID {,'/{S*/,}'}'L*/{,Co*/*/*/L*/}{Cache,Log}s $TMPDIR../C -type f -size +'${p[11]}'M -exec stat -f'%z:%N' {} \;' \ /v*/d*/*/*l*d{,.*.$UID}/* '-app Safari UserStyleSheetEnabled' 'L*/A*/Fi*/P*/*/a*.json' users/$USER\ HomeDirectory '{/,}L*/{Con,Pref}* -type f ! -size 0 -name *.plist -exec plutil -s {} \;' ' -F "\$Time \$(Sender): \$Message" -k Level Nle 3 -k Facility R'{'ne "user|','eq "'}'console" -k Message CRne "[{}<>]|commit - no t|deprec|Goog|realp|sandbox ex|/root" ' getenv '/ "kMDItemDateAdded>=\$time.now(-'${p[23]}')&&kMDItem'${k[33]}'=*"' -m\ / '' );N1=${#c2[@]};for j in {0..20};do c2[N1+j]=SP${k[j]}DataType;done;l=({Restricted\ ,Lock,Pro}files POST Battery {Safari,App,{Bad,Loaded}\ kernel,Firefox}\ extensions System\ load boot\ args FileVault\ {2,1} {Kernel,System,Console}\ log Activity SMC Login\ hook 'I/O per process' 'High file counts' UID Daemons Agents XPC\ cache Startup\ items {Admin,Root}\ access Stylesheet Library\ paths{,' ('{shell,launchd}\)} Font\ issues Firewall Proxies DNS TCP/IP Wi-Fi 'Elapsed time (sec)' {Root,User}\ crontab {Global,User}' login items' Spotlight Memory\ pressure Listeners Widgets Parental\ Controls Prefetching Nets Volumes {Continuity,I/O,iCloud,HID,HCI}\ errors {User,System}\ {caches/logs,overrides} Shutdown\ codes Heat Diagnostic\ reports Bad\ plists Free\ space VM Bundles{,' (new)'} Trust\ settings );N3=${#l[@]};for i in {0..8};do l[N3+i]=${k[5+i]};done;F() { local x="${s[$1]}";[[ "$x" =~ ^([\&\|\<\>]|$) ]]&&{ printf "$x";return;};:|${c1[30]} "$x" 2>&-;printf "%s \'%s\'" "|${c1[30+$?]}" "$x";};A0() { Q=6;v[2]=1;id -G|grep -qw 80;v[1]=$?;((v[1]))||{ Q=7;sudo -v;v[2]=$?;((v[2]))||Q=8;};v[3]=`date +%s`;date '+Start time: %T %D%n';printf '\n[Process started]\n\n'>&4;printf 'Revision: %s\n\n' ${p[0]};};A1() { local c="${c1[$1]} ${c2[$2]}";shift 2;c="$c ` while [[ "$1" ]];do F $1;shift;done`";((P2))&&{ c="sudo $c";P2=;};v=`eval "$c"`;[[ "$v" ]];};A2() { local c="${c1[$1]}";[[ "$c" =~ ^(awk|sed ) ]]&&c="$c '${s[$2]}'"||c="$c ${c2[$2]}";shift 2;local d=` while [[ "$1" ]];do F $1;shift;done`;((P2))&&{ c="sudo $c";P2=;};local a;v=` while read a;do eval "$c '$a' $d";done<<<"$v";`;[[ "$v" ]];};A3(){ v=$((`date +%s`-v[3]));};B1() { v=No;! ((v[1]))&&{ v=;P1=1;};};eval "`type -a B1|sed '1d;s/1/2/'`";B3(){ v[$1]="$v";};B4() { local i=$1;local j=$2;shift 2;local c="cat` while [[ "$1" ]];do F $1;shift;done`";v[j]=`eval "{ $c;}"<<<"${v[i]}"`;};B5(){ v="${v[$1]}"$'\n'"${v[$2]}";};B6() { v=` paste -d$'\e' <(printf "${v[$1]}") <(printf "${v[$2]}")|awk -F$'\e' ' {printf("'"${f[$3]}"'",$1,$2)} ' `;};B7(){ v=`egrep -v "${v[$1]}"<<<"$v"|sort`;};eval "`type -a B7|sed '1d;s/7/8/;s/-v //'`";C0() { [[ "$v" ]]&&sed -E "$s"<<<"$v";};C1() { [[ "$v" ]]&&printf "${f[$1]}" "${l[$2]}" "$v"|sed -E "$s";};C2() { v=`echo $v`;[[ "$v" != 0 ]]&&C1 0 $1;};C3() { B4 0 0 63&&C1 1 $1;};C4() { echo $'\t'"Part $((++P)) of $Q done at $((`date +%s`-v[3])) sec">&4;};C5() { sudo -k;pbcopy<<<"$o";printf '\n\tThe test results are on the Clipboard.\n\n\tPlease close this window.\n';exit 2>&-;};for i in 1 2;do eval D$((i-1))'() { A'$i' $@;C0;};';for j in 2 3;do eval D$((i+2*j-3))'() { local x=$1;shift;A'$i' $@;C'$j' $x;};';done;done;trap C5 2;o=$({ A0;D0 0 N1+1 2;D0 0 $N1 1;B1;C2 27;B1&&! B2&&C2 28;D2 22 15 63;D0 0 N1+2 3;D0 0 N1+15 17;D4 3 0 N1+3 4;D4 4 0 N1+4 5;D4 N3+4 0 N1+9 59;D0 0 N1+16 99; for i in 0 1 2;do D4 N3+i 0 N1+5+i 6;done;D4 N3+3 0 N1+8 71;D4 62 1 10 7;D4 10 1 11 8;B2&&D4 18 19 53 67;D2 11 2 12 9;D2 12 3 13 10;D2 13 32 70 101 25;D2 65 6 76 13;D2 45 20 52 66;D4 66 7 77 14;D4 17 8 15 38;D0 9 16 16 77 45;C4;B2&&D0 35 49 61 75 76 78 45;B2&&{ D0 28 17 45;C4;};D0 12 40 54 16 79 45;D0 12 39 54 16 80 45;D4 31 25 77 15&&{ B4 0 8 103;B4 8 0;A2 18 74;B6 8 0 3;C3 32;};B2&&D4 19 21 0;B2&&D4 40 10 42;D2 2 0 N1+19 46 84;D2 44 34 43 53;D2 25 22 20 32;D2 33 0 N1+14 51;for i in {0..2};do A1 29 35+i 104+i;B3 25+i;done;B6 25 27 5;B6 0 26 5;B4 0 0 110;C2 69;D2 34 21 28 35;D4 35 27 29 36;A1 40 59 81;B3 18;A1 33 60 82;B8 18;B4 0 19 83;A1 27 32 39&&{ B3 20;B4 19 0;A2 33 33 40;B3 21;B6 20 21 3;};C2 36;D4 50 38 5 68;B4 19 0;D5 37 33 34 42;B2&&D4 46 35 45 55;D4 38 0 N1+20 43;B2&&D4 59 4 65 76 91;D4 63 4 19 44 75 95 96;B1&&{ D4 53 5 55 75 69&&D4 51 6 58 31;D4 56 5 56 97 75 98&&D0 0 N1+7 99;D2 55 5 27 84;D4 61 5 54 75 70;D4 14 5 14 12;D4 15 5 72 12;C4;};D4 16 5 73 12;A1 13 44 74 18;C4;B3 4;B4 4 0 85;A2 14 61 89;B4 0 5 19 102;A1 17 41 50;B7 5;C3 8;B4 4 0 88;A2 14 24 89;C4;B4 0 6 19 102;B4 4 0 86;A2 14 61 89;B4 0 7 19 102;B5 6 7;B4 0 11 73 102;A1 18 31 107 94 74||{ B2&&A1 18 26 94 74;}&&{ B7 11;B4 0 0 11;C3 23;};A1 18 26 94;B7 11;B4 0 0 11;C3 24;D4 60 14 66 92;D4 58 14 67 93;D4 26 4 21 24;D4 42 14 1 62;D4 43 37 2 90 48;D4 41 10 42;D2 48 36 47 25;A1 4 3 60&&{ B3 9;A2 14 61;B4 0 10 21;B4 9 0;A2 14 62;B4 0 0 21;B6 0 10 4;C3 5;};D4 9 41 69 100;D2 29 21 68 35;D2 49 21 48 49;B4 4 22 57 102;A1 21 46 56 74;B7 22;B4 0 0 58;C3 47;D4 54 5 7 75 76 69;D4 52 5 8 75 76 69;D4 57 4 64 76 91;D2 0 4 4 84;D2 1 4 51 84;D4 21 22 9 37;D0 0 N1+17 108; A1 23 18 28 89;B4 0 16 22 102;A1 16 25 33;B7 16;B4 0 0 34;D1 31 47;D4 64 4 71 41;C4;B4 4 12 26 89 23 102;for i in {0..3};do A1 0 N1+10+i 72 74;B7 12;B4 0 0 52;C3 N3+5+i;((i))||C4;done;A1 24 22 29;B7 12;B3 14;A2 39 57 30;B3 15;B6 14 15 4;C3 67;A1 24 75 74;B3 23;A2 39 57 30;B3 24;B6 23 24 4;C3 68;B4 4 13 27 89 65;A1 24 23;B7 13;C3 30;B4 4 0 87;A2 14 61 89 20;B4 0 17;A1 26 50 64;B7 17;C3 6;D0 0 N1+18 109;D4 7 11 6;A3;C2 39;C4;} 4>&2 2>/dev/null;);C5
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