root or subdirectory?

[fakeDecoy]

On a website that only hosts zencart without other content, what's better, installing zencart in the root, or in a /store/ subdirectory?

I currently have it in the root, but it's a pain to test an upgrade or mod and switch over to the new version when ready. I have to upload the new version twice - once to test, and once again in the root to go live. I have a lot of media files, so it takes hours, and doing it twice takes all day. The advantage I see with a subdirectory is ease of testing upgrades/mods and switching over very quickly by simply renaming the folders and swapping the configure.php files. It also would let me switch back to the old one quickly if something goes wrong.

What are the disadvantages of having a subdir? A shorter URL length for user-friendly purposes doesn't seem to make sense, because the zc URLs to product pages are already so long that nobody is going to be trying to remember them and typing them out, and they already often get broken in emails due to the length.

If I change it to /store/, I might do something to invisibly redirect the root to /store/ so that the URL remains shorter. Is there any disadvantage to doing that? Any special considerations given that my store is currently in the root and I don't want to lose traffic?