I want to update a Typo3 installation from 4.5.29 to 4.5.39.
In the current installation I don't have typo3_src or any other symlinks. Typo3 is directly in the httpdocs.
I know newer Versions (6.2.*) can be ugpraded by adding the new typo3_src and change the link to the new one. But for this case I did not find a manual or howto.
I downloaded the blankpackage-5.4.39. How do I upgrade my typo3 installation now? Can I just copy the folders t3lib and typo3 into my installation?
You have to replace the folder t3lib, typo3 and the file index.php with the files from the new core, then clear all caches. That should be it.
But don't just copy the new folders over, remove them (maybe rename first in case you need to switch back). Leaving them in place could leave vulnerable files from before security patches.
While you are on it, you can as well switch to use symlinks to make it easier in the future. No TYPO3 6.2 needed for that, symlinks work fine for older versions. Just download the new core to some folder, create a symlink named typo3_src to that folder in your installation root. Then replace typo3, t3lib and index.php with symlinks to typo3_src/typo3, typo3_src/t3lib or typo3_src/index.php, respectively.