In version 6.0.1+, many root files are no longer needed. Please go through the list below and decide whether or not you want to keep those files. It is recommended to delete all files you don’t need:

• a_noskin.php – if you needed this, you would know. Otherwise, delete it.
• a_stub.php – if you needed this, you would know. Otherwise, delete it.
• blog1.php – keep this only if one of your collections includes /blog1.php in its URL. If it’s the case you may also want to change the URL to something cleaner and delete this file.
• blog2.php – keep this only if one of your collections includes /blog2.php in its URL. If it’s the case you may also want to change the URL to something cleaner and delete this file.
• blog3.php etc. – same as above.
• contact.php– if you have not manually created a link to this page, you don’t need it. Delete it.
• crossdomain.xml– No longer used. Delete it.
• default.php – this file is useful for beginners when they haven’t configured their first collection yet. If you’re past this step, delete this file.
• index_multi.php – Everything is handled by index.php now. Delete it.
• multiblogs.php – if you needed this, you would know. Otherwise, delete it.
• sitemap_a.php – if you needed this, you would know. Otherwise, delete it.
• sitemap_blogs.php – if you needed this, you would know. Otherwise, delete it.
• summary.php – if you needed this, you would know. Otherwise, delete it.

It is also strongly advised to delete any _html_header..inc.php found in any /skins/name_of_skin/ folder. It will most likely NOT be compatible with b2evolution 6 and create side effects that will be hard to track down. Better delete it and if the skin breaks because of that, you know you need something new ;)