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However this shortlink is 301'ed (moved permanently) via mod_rewrite to subdomain.domain.com/folder/ as this is my (root) in the context of the running application
Moving my root is not an option.
My question is, is it considered a bad practice to link to a URL that you have setup as a 301 ?
Thanks in advance
Chained redirects are definitely one to avoid (i.e. redirecting to a URL that then redirects again).
Moving my root is not an option
Remember that you don't need to physically move a folder to hide it from URL requests. If the subfolder is superfluous to requirements (for instance if it's more about the underlying technology than a useful path for visitors, like subdomain.domain.com/cms/) then you could use mod_rewrite to serve content from subdomain.domain.com/ without the extra directory.
If that's sounds useful, you could have a go at the rewriting and then post over in the Apache forum if you run into problems.
Here is an example of my root:
/folder (this is my main application which I redirect root to)
folder2-4 are my assets folders that contain a lot of other stuff that the main application needs/refers to. Therefore moving my root logically or physically to folder is not possible. Or let me rephrase that, everything is possible, I just dont think that it would be justifiable with the amount of work needed...
ibm.com does a 301 to a folder
microsoft.com does a 301 to a folder
godaddy.com does a 302 to a folder (and the new url has no pagerank - maybe due to the 302 or because its a new page)
forums.bimmerforums.com does a 301 to a folder (no pagerank for new url)
www.accenture.com does a 301 to a folder
www.cocacola.com does a 301 to a folder
www.elsevier.com does a 200 to a folder (using meta tag) and has PR9 (this is how i previously did my redirect)
[answers.google.com...] does a 301 to a folder
www.blogger.com does a 302 to a folder
I'd say if so many large companies is doing a 301 from root to a folder, little me should be ok :-)