3.0 Upgrade Tool not updating files

Morning,

I've ran a few passes with the upgrade tool on a cake 2 project and have found the running bin/cake upgrade all /var/www/app my Model files are not relocated. Running through the various upgrade commends individually does relocate my Models. That is really just a comment, the current issue I have is as follows.

After running the upgrade tool in full, although I can see that my controllers/models/views and so forth have been relocated, my index.php and .htaccess in webroot go unchanged. I do not see any permission related errors from the upgrade tool and the directories and files have permissions to write these files.


I can of course update index.php and .htaccess manually however this leads me to believe perhaps other files have not been created/updated and leads me to my 2 questions..


1. Do the old 2 project files get automatically removed after the upgrade or do we need to remove them manually?
2. Can anyone think of a reason the index.php and .htaccess files are not being upgraded?


Many thanks
James

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