Now there are some plugins that require .htaccess modifications,but most of those are uri rewriters. I don't know of any that specifically need .htaccess mods. Okay there are those things that will need a different type of file to be accessible such as .csv files in certain directories, some sort of multimedia upload/download. But most of those extra facts are covered in the applicable installation instructions or in a FAQ or the wiki. Then of course in the forum thread for that application, etc...
Anyways, the instructions do leave details to be determined and are written to provide a more grand overview. Many have asked the question of upgrade details, and many have responded, typically each with a little of this or a little of that different, but generally coming back to the same base instruction. While version 1.3.8 may not have been as "portable" as the later versions, if the site was originally built under the current philsophy of change as little of the default code provided and use the override system as much as possible, then upgrades are far easier/quicker and less buggy. It's when holding onto what was and may no longer work with the current code (more secure) that issues begin to crop up.
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