How to remove "/magento/" and "/index.php/" showing in internal links and dup pages in GWT

[GarGar]

This post is deleted!

[Milian]

Hey GarGar, if you would like to post a link to your site it would be easier to have a look at the issues.

[GarGar]

Hey Maximillian,

http://www.gemeinhardt.com

Thanks

[customerparadigm.com]

We dealt with this with a major eCommerce site in the home decorating world in the past, and did a ton of technical backflips to correct this.

My $0.02, though, is that you should consider moving all of the files from the /magento/ directory back up to the html root, as this should fix everything for you.  (Although you'll need to deal with the server re-writes and things you've put into place to mask this.)

We do a tremendous amount of Magento work as a Magento Silver Solutions Partner, but I'd highly recommend physically moving the files to fix this.  There's a lot of stuff behind the scenes that Magento does with indexing and file management.

[GarGar]

Thanks Jeff.

Unfortunately moving folders right now are out of the question due to a slew of other projects that have to get done — possibly for a future project. Although I have found out that by calling links in blocks with "{{store url=""}}" as opposed to "{{store direct_url=""}}" yields different url results (but the same content), so I've updated all calls to links which did drop some of my duplicate pages. I'm not to savvy on the various ReWrite/conditions with .htaccess, but will play around with some of them to see if they yield different results. It just sucks that whatever changes I do won't always be updated right away in Google's index. Thanks again for your advice.

EDIT:
I've also become VERY attentive to all of the installed extensions now because I've noticed how many aren't that optimized for SEO out of the box. They end up creating duplicate content with dynamically generated urls along with the ones you manually establish in the extension itself; Commerce Lab News being one of them.

[GarGar]

Well after four score and twenty other solutions I tried, I eventually tried a solution that my web hosting company suggested.

They created a bogus domain name for me and pointed it to the root folder. The only drawback to that is that our billing account goes by the bogus domain name instead of the main domain name... yeah... boo hoo right? Lol

Then they made our main domain name point to the magento subfolder via the dns zone records. That way I'm able to treat Magento as if it's a root folder install, but still keep it in a sub-directory. I get to keep my actual root folder free from magento installation files, and there are NO complex .htaccess rewrite rules, or modifications to the /magento/index.php page either. All in all, it's a great, fast and easy solution to the issue I was having. :)))