Not sure if this is a bug or not.
With the new Upload to Server in v.13, I have been given mixed instructions. Some tech support advisors have said that it's Ok to drop a file into its correct folder and not worrry about setting the permissions the way the old Java client did when it was used to Upload to Server. I've tried it both ways, without any significant problems ... until today. Here's what I did and what I observed:
In FileMaker Server, I closed the file in order to do some maintenance. Specifically, I needed to implement remote container storage for a field that had previously stored document files in a container field. Everything went properly with the transfer of the container storage.
Then, before closing the file, I thought it would be wise to save a compacted copy, which would reduce the file size significantly ahving removed all the embedded container data. I saved the compacted copy to the same location as the file itself, resulting in a new file with the name Copy added.
Then, I removed the original file from the directory, changed the file name of the new version to delete the word Copy, and re-opened the file in FMS. All my work was done with the both files in their proper FMS directory.
When the file was re-opened, I found that Manage Scripts was not available to me with Full Access privileges. I also found that other menu commands such as Manage Database were dimmed in their menus. I made certain that Standard FileMaker Menus was chosen in the Tools menu.
I then closed the file, moved it to the desktop and uploaded it to FMS using FileMaker Advanced. That fixed it.
I believe this issue is repeatable because it happened to me yesterday when I did something similar, transfering a file from an older FMS-12 server to a new FMS-13 server via FTP. Had to do it that way because I don't have a copy of Pro or Advanced on the old server. When I dropped the file into place on the new server, I had these menu/permissions issues. When I uploaded the file to the Server using the client software, it was OK.