Upgrading Drupal

In the upgrade instructions, you are told to Copy the new sources over the old ones. But it was also previously stated not to overwrite your original 4.4 files with the new install. It would be extremely useful if an illustrative command could be given or more instruction on how to do this, because "Copy the new sources" is really a shortcut for a process that for some is not 100% apparent.

I have quite a few problems. Go to http://nickmade.com to see. It can't load the themes and MANY links don't work :(

Hello everyone,

I recently upgraded my 4.4.2 drupal site with the latest 4.5 CVS version. Everything went OK, with one notable exception - when I want to create content - be it a story, page, poll or image - I only see the "Preview" button, but not the "Submit" one. As such, I can't create new content; I can only look at it and appreciate its beauty :)

When running upgrade.php i got this error " Warning: mysql_connect(): Unknown MySQL Server Host 'mysql' (2) in /*****/********/public_html/nickkarstedt/phportal/includes/database.mysql.inc on line 31
Unknown MySQL Server Host 'mysql' (2) " Please help. I put " * "'s to filter what i can show you, it didnt show the stars in the message

I have two problems with my upgrade at http://www.pennywit.com. First is that a number of comments have the body turn to the number 3. It looks like this happens when one of my users tries to edit his comments. The second is that in any nodes submitted before I upgraded, I don't see a count of the comments already submitted. I filed a bug report. Any ideas how to remedy it here?

I just upgraded to the 4.5.0RC and things are lovely, except the header links that i had set for custom pages have disappeared. The defaults are there, but not the ones I created for pages I added. Also, when creating a new page, there is no longer the option to create a headerlink with it. Anyone?