Upgrade MySQL 4.0.27 to MySQL 5.0.51a
This guide explained it very well, just follow it.

Note:
1. mysql_upgrade will repair tables automatically when needed.

2. After running mysql_upgrade, mysql server should be restarted.

3. mysql_upgrade can be executed more than one time with the '-f' option. e.g. if you see lots of errors during mysql_upgrade, you may want to make sure all tables are OK.

Upgrading PHP 4.4.8 to 5.2.5
I started with this guide, but I didn't use portupgrade for such major upgrades. Anyway, it's basically the same, list all PHP related packages, delete them first, install them manually.

Note:
1. It seems that lang/php5-extensions has included all PHP related packages, just check those you required.

2. Apache configuration file needs some changes:
DirectoryIndex: I simply replaced 'php4' with 'php5'
AddType: Added the following lines:

<IfModule mod_php5.c>
AddType application/x-httpd-php .php
AddType application/x-httpd-php-source .phps
</IfModule>

I wish everyone a happy and fruitful new year!

- The Apache error often pops up without a clue. It seems caused by the settings of 'Debug Dialog'.

Here are the screenshots of the workable settings.

- Debug a PHP script, execute a PHP script directly.
This is very easy, just install Zend Executable Debugger. I installed it with the update mode.

- Debug a PHP Web page, through a web server
In the PDT installation guide, Zend Web Server Debugger links to Zend Platform - a commercial product. Actually Zend does offer a free server debugger, but there is no Windows version, is the cygwin version for Windows? Maybe I should try it before XDebug.

- My every XDebug attempt ended with a clueless Apache application error, the breakpoint made the debug stop, but one more step crashed the debug process. I tried to change Apache configuration and other trivia with the help of XDebug Support In PDT (A must read for XDebug config), I don't know the exact problems, it suddenly worked magically.

Anyway, Eclipse is ready and looks great, I will continue reading my online book. I believe learning PHP with a powerful IDE would be fun.

My first step was to find a good book. After some searching, I decided to use Practical PHP Programming. Just after reading a few pages I was convinced this is a great book, it elaborated a few issues very well such as quotes and heredoc, I was always confused about them but have never taken the time to solve them. The author seems to have lots of experience and knows exactly what's important for beginners.

The second step is IDE. Coddled by VC++ and VAJ (my favorite), I can't code without a good IDE, should I blame myself for that? First I installed Zend Studio, it looks pretty good to me, but soon I found Eclipse supports PHP as well, I installed it immediately. Back in 2002, one of my colleagues
was a fan of Eclipse, since it can compete with VAJ, it must be really good :-). After the code-assist window pops up, I know Eclipse is my final choice.

Stay tuned!

Update ports tree
# portsnap fetch update

For complete guide, check out the handbook "Using Portsnap".

I tried Privoxy. It's very easy to use and worked well.

Installation
# cd /usr/ports/www/privoxy
# make install clean
# rehash

The configuration file is /usr/local/etc/privoxy/config, there is one line which must be changed:
listen-address 127.0.0.1:8118
The IP should be changed to your server's IP address. Also, it's better to use a non-default port number for security reasons.

Start Privoxy
# privoxy /usr/local/etc/privoxy/config

Now you can configure your browser or other Internet software with the listen-address configured above.

> ad0: FAILURE - READ_DMA status=51<READY,DSC,ERROR> error=40<UNCORRECTABLE>
LBA=154033791
> ad0: FAILURE - READ_DMA status=51<READY,DSC,ERROR> error=40<UNCORRECTABLE>
LBA=154033791
> ad0: FAILURE - READ_DMA status=51<READY,DSC,ERROR> error=40<UNCORRECTABLE>
LBA=154033791
> ad0: FAILURE - READ_DMA status=51<READY,DSC,ERROR> error=40<UNCORRECTABLE>
LBA=150991359

Apache started to generate fatal errors too since two days ago:
> pid 81205 (httpd), uid 80: exited on signal 10
> pid 82339 (httpd), uid 80: exited on signal 10
> pid 81204 (httpd), uid 80: exited on signal 10
> pid 88426 (httpd), uid 80: exited on signal 10
> pid 89324 (httpd), uid 80: exited on signal 10
> pid 81207 (httpd), uid 80: exited on signal 10
> pid 88654 (httpd), uid 80: exited on signal 10

Combined these two errors, it's very likely a hard disk problem. I contacted my ISP (LayeredTech), the tech support confirmed: "DMA errors with the UNCORRECTABLE code are almost always evidence of a failing drive."

He suggested a system reload on a new hard disk. But rebuilding the system with a dozen websites might take a few hours or even longer, I really want to avoid such a down time. I decided to order a new server and cancel the current one after finish the transfer. LayeredTech is very understanding and cooperative with prompt response, I am very satisfied.

# cd /usr/ports/graphics/php4-gd
# make install clean
# apachectl graceful

If a PHP script needs gd module but can't find it, it will display the following error:
Fatal error: Call to undefined function: imagecreatefromjpeg()

P.S. A simple problem could be troublesome for newbies if they can't find the right web pages. When searching the solution to the above error, a FreeBSD user may be led to a Linux page which states that PHP must be recompiled with gd support. But this is not applicable for FreeBSD system. Hopefully, after I blog this problem, Google will lead them to this post, so that they can enable gd support for PHP within minutes without touching the main PHP installation.

1. Must enable MySQL in /etc/rc.conf.
The following line must be present in /etc/rc.conf:
mysql_enable="YES"

Without this line, "/usr/local/etc/rc.d/mysql-server.sh start" will quit without any errors or warnings. It took me a few hours to figure this out...a simple reminding message would be very helpful.

For a complete list of parameters which can be specified in rc.conf, please refer to mysql-server.sh (appended below).

2. MySQL runs as mysql user instead of root.
Great change.

3. my.cnf is moved from /etc/ to /usr/local/etc/.
Good change. This can avoid confusions since /etc/my.cnf is Linux style.

=======================================
Content of /usr/local/etc/rc.d/mysql-server.sh

# PROVIDE: mysql
# REQUIRE: NETWORKING SERVERS
# BEFORE: DAEMON
# KEYWORD: shutdown

#
# Add the following line to /etc/rc.conf to enable mysql:
# mysql_enable (bool): Set to "NO" by default.
# Set it to "YES" to enable MySQL.
# mysql_limits (bool): Set to "NO" by default.
# Set it to yes to run `limits -e -U mysql`
# just before mysql starts.
# mysql_dbdir (str): Default to "/var/db/mysql"
# Base database directory.
# mysql_args (str): Custom additional arguments to be passed
# to mysqld_safe (default empty).
#

. /etc/rc.subr

name="mysql"
rcvar=`set_rcvar`

load_rc_config $name

: ${mysql_enable="NO"}
: ${mysql_limits="NO"}
: ${mysql_dbdir="/var/db/mysql"}
: ${mysql_args=""}

mysql_user="mysql"
mysql_limits_args="-e -U ${mysql_user}"
pidfile="${mysql_dbdir}/`/bin/hostname`.pid"
command="/usr/local/bin/mysqld_safe"
command_args="--defaults-extra-file=${mysql_dbdir}/my.cnf --user=${mysql_user} --datadir=${mysql_dbdir} --pid-file=${pidfile} ${mysql_args} > /dev/null &"
procname="/usr/local/libexec/mysqld"
start_precmd="${name}_prestart"
mysql_install_db="/usr/local/bin/mysql_install_db"
mysql_install_db_args="--ldata=${mysql_dbdir}"

mysql_create_auth_tables()
{
eval $mysql_install_db $mysql_install_db_args >/dev/null 2>&1
[ $? -eq 0 ] && chown -R ${mysql_user}:${mysql_user} ${mysql_dbdir}
}

mysql_prestart()
{
if [ ! -d "${mysql_dbdir}/mysql/." ]; then
mysql_create_auth_tables || return 1
fi
if checkyesno mysql_limits; then
eval `/usr/bin/limits ${mysql_limits_args}` 2>/dev/null
else
return 0
fi
}

run_rc_command "$1"

-----------------------------------
4.0.21, doesn't care about rc.conf
-----------------------------------

#!/bin/sh

DB_DIR=/var/db/mysql
PIDFILE=${DB_DIR}/`/bin/hostname -s`.pid

case "$1" in
start)
if [ -x /usr/local/bin/mysqld_safe ]; then
/usr/bin/limits -U mysql \
/usr/local/bin/mysqld_safe --user=mysql --datadir=${DB_DIR} --pid-file=${PIDFILE} > /dev/null &
echo -n ' mysqld'
fi
;;
stop)
if [ -f ${PIDFILE} ]; then
/bin/kill `cat ${PIDFILE}` > /dev/null 2>&1 && echo -n ' mysqld'
else
echo "mysql-server isn't running"
fi
;;
*)
echo ""
echo "Usage: `basename $0` { start | stop }"
echo ""
exit 64
;;
esac

PHP Warning: Unknown(): Unable to load dynamic library '/usr/local/lib/php/20020429/xml.so' - Shared object "libexpat.so.5" not found, required by "xml.so" in Unknown on line 0

Reinstalling /usr/ports/textproc/php4-xml fixed it.

Finally I took the time to upgrade all vulnerable packages reported by portaudit and gave Mambo another try, the latest version 4.5.3 seems to work well.

The version numbers of involved packages:
apache-1.3.34_4
php4-4.4.2_1
mysql-server-4.0.26

I didn't install Mambo via ports, for PHP scripts, I prefer manual installation. Since we usually need to customize the script a lot, ports will only make the upgrade more complicated.

I know little about shell scripts, let me start from an easy one - AwStats.

Name the update script as "awstats_update_all.sh" with the following content:
#!/bin/sh
cd /usr/local/www/awstats/tools/
./awstats_updateall.pl now -awstatsprog=/usr/local/www/awstats/cgi-bin/awstats.pl

The script is also an ideal place to syncronize the server time, ntpd is overkill with annoying output.
/usr/sbin/ntpdate pool.ntp.org

I also want to know the execution time, so my complete version is:
#!/bin/sh
cd /usr/local/www/awstats/tools/
date
./awstats_updateall.pl now -awstatsprog=/usr/local/www/awstats/cgi-bin/awstats.pl
date
/usr/sbin/ntpdate pool.ntp.org

Put it in cron job, update daily at 2:01am:
01 02 * * * /home/some_account/awstats_update_all.sh

Let me use this blog as an example to explain the problem. This blog can be accessed by typing freebsdblog.org or www.freebsdblog.org in your browser, there is no any difference to you. But Google treats them as two different websites, since they have exactly the same content, Google may dump out one of them due to duplicated content penalty. If Google bans the one you have been promoting, that would be a big problem.

This may sound very silly, but it has been discussed for years and reported by many webmasters. Recently, my sites also had some problems like this, although I'm not very sure about the reasons. If you try Yahoo, Google, MSN or FreeBSD, all of the big guys redirect you to the www version with permanent redirection (HTTP 301). Anyway, I strongly suggest you configure your domains this way, by which you will only benefit from it:

2. All your back links will help your search engine ranking whether they point to www or non-www version.

Solution
This can be configured with .htaccess or httpd.conf.

.htaccess
Make a file name ".htaccess" with the following content and put it in the DocumentRoot directory. If there are other .htaccess in any sub-directories, they should be modified too:

RewriteEngine on
RewriteCond %{HTTP_HOST} ^freebsdblog.org
RewriteRule (.*) http://www.freebsdblog.org/$1 [R=301,L]

httpd.conf
If you have access to the main Apache configuration file, you can configure it in the domain level, which is a much more elegant solution:

<VirtualHost 72.21.48.122>
ServerAlias freebsdblog.org
ServerAdmin your_email_address
DocumentRoot /home/freebsd/www
ServerName www.freebsdblog.org
RewriteEngine On
RewriteCond %{HTTP_HOST} !^72.21.48.122(:80)?$
RewriteCond %{HTTP_HOST} !^www.freebsdblog.org(:80)?$
RewriteRule ^/(.*) http://www.freebsdblog.org/$1 [L,R=301]
ErrorLog /var/log/www/freebsdblog.org-error_log
CustomLog /var/log/www/freebsdblog.org-access_log combined
</VirtualHost>