Update wordpress manually step-by-step
1. Disable all your plugin and change template to default wordpress.
2. Logon to SSH using your favorite SSH Client.
3. Download your favorite blog by using the following line :
me@einsamsoldat.net [~/public_html]#wget http://wordpress.org/latest.zip
4. After step 3 is done, backup your wordpress database and wordpress files (assuming your blog created in subfolder blog) :
me@einsamsoldat.net [~/public_html]#cd blog
me@einsamsoldat.net [~/public_html/blog]#mysqldump -umydb_user -ppassword > mydb.sql
me@einsamsoldat.net [~/public_html/blog]#cd ..
me@einsamsoldat.net [~/public_html]#tar -czvf backup_blog.tar.gz blog/
5. Once step 4 is done, means you have done backup your current blog. Its time for upgrade. Remember the file we downloaded using wget from step 3. It is time to extract the file :
me@einsamsoldat.net [~/public_html]#tar -xzvf latest.tar.gz
6. New files being extracted, it is really time to upgrade.
me@einsamsoldat.net [~/public_html]#cd blog
me@einsamsoldat.net [~/public_html/blog]#cp wp-config.php wp-config.bak
me@einsamsoldat.net [~/public_html/blog]#rsync -avz ../wordpress/wp-includes/* wp-includes/
me@einsamsoldat.net [~/public_html/blog]#rsync -avz ../wordpress/wp-admin/* wp-admin/
me@einsamsoldat.net [~/public_html/blog]#rsync -avz ../wordpress/*.php ./
me@einsamsoldat.net [~/public_html/blog]#cp wp-config.bak wp-config.php
7. Done ? Not really, the replacement of vital files is done but you will need to visit your site to finish the database upgrade. In my case, I need to go http://www.einsamsoldat.net/blog/wp-admin . Click “Upgrade” button.
8. Congrats, you have successfully upgraded your wordpress manually.
*Note : This step is derived from the original wordpress upgrade codex.