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Meaning the upgrade from 4.4.2 to 4.4.3 should be easy?
Or is it better to install 4.4.4 then apply the skin manually, in code line by line if it works?
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I would not use the word "easy" about any upgrade, minor or major, until you see the upgrade pack. The possibilities are wide open. There could many relatively easy changes to a large number of files, few complex changes to few files or any combination of those possibilities. The other important factor is the number and scope of changes that you have made to your own skins & php files. If you understand all the changes that were made, that puts you at an advantage if/when the upgrade requires similar changes near your own modifications. Another factor is patches. If you have already applied patches, the upgrade will attempt to re-apply them.
Another possibility is that all your customizations are to files not impacted by the files in the upgrade - then you don't have to worry about the tedium of looking at the diff files.
Even when changes are easy, upgrades are almost always tedious. The best approach for you to take depends on the above factors plus your own patience and understanding of your customizations.
For past upgrades, on heavily modified shops - I find it best to get a report of the could not patch files, then patch them one by one looking at the diff files provided in the patch. If the shop is not heavily modified, the QT upgrade kits get you almost all the way there. Then you can use the word "easy". The more customizations you have done - the more tedious you can expect the upgrade to be.
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would it be possible for qualiteam to simply list which files have had modifications made to them?
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This list has been a part of the upgrade kits in the past (file.lst). In addition to the upgrade links provided by QT above - I have found this sticky post to contain very good advise about upgrading:
http://forum.x-cart.com/showthread.php?t=35125
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