#3 Why are blocks being deactivated on my site? Why is my copy site acting strangely?
If you copy an entire site in order to split apart some of its content, make sure you investigate the cache folder and remove any remnant of the previous site cache. There may be a folder for the previous site.
Otherwise, for a little period of time, you’ll be getting some strange behavior that makes it seem like the old site is still hanging around on the new install.
Even if that description didn’t make sense, if you are having strange theme behaviors that flushing the cache, rebuilding permissions and/or a restart don’t seemed to have fixed… check out the cache folder on your server.
Additionally, if you a splitting a site into two, and intend to use both sites on the same machine, and in the same database instance(ie, two databases on the same machine), make sure you check that the copy site isn’t pointing to any shared folder on the server, ie your cache folder. If somehow, both sites are using the same cache folder, changes on one site may affect the other site.
You are better off changing your site into a multi-site instance, for Drupal 7, because that should mitigate most of these problems. Multi-sites use different cache/files directories unless explicitly sharing modules/themes/frameworks out of the sites/all folder.
#4 git loses track/won’t overwrite settings.php file. (combo drupal + git tip)
error: unable to unlink old 'sites/default/settings.php' (Permission denied) fatal: Could not reset index file to revision 'origin'.
Repairing/resetting my mac home directory permissions seemed to fix things. ( Resolve issues caused by changing the permissions of items in your home folder )