This is a question that has bugged me for a really long time and I realize this it isn't necessarily related to WordPress, however I wanted to start by asking the WordPress community. I've been selling WordPress themes for a couple of years now and this is an issue that has come up repeatedly in dealing with customer support but have never really known how to address it, or if it's something I'm doing wrong or not.
The problem that leads me to ask
Every once in awhile when someone installs one of my themes, they decide to go the route of unzipping it and manually uploading the theme folder to wp-content/themes/ of their site with their FTP client.
When people do this they often run into the same issue and it is this: Things on their site will end up not working because it ends up turning out that there are certain files of the theme that when uploaded received permissions that are not readable on their web server...
For the longest time I've chalked this up to inexperience on the user's part. I tell them to change the file permissions with their FTP program. They figure out what the heck that means, and all is right.
However this is continuing to happen to people, and I'm having to give the same responses again and again. Now I'm starting to see more of a pattern with which files it's happening to for people and seeing that it's the same files again and again.
Another thing to note is I've noticed that this happens the most with files I've pasted into the theme. For example, I include the pretty photo jQuery plugin where I've just pasted the folder from prettyPhoto in there and users often end up with the pretty photo CSS and JS file that have non-readable file permissions.
I understand that users are not experienced with troubleshooting these issues and are not savvy with finding a file that has been give improper permissions, but the fact that users keep facing this with the same files leads me to believe that this is something I'm doing on my end with the files.
So, is this possible? What theoretically could I being doing with plain 'ol CSS, JS, and PHP files on my end that could result in a user uploading the theme on their end with these certain files receiving weird file permissions?
I'm not sure if this is relavant or not, but I do all my work with these files in Coda on Mac OS 10.7, working with MAMP on my localhost.