MacOS – Clean install Mac, restore backup without command line tools

It's not that simple as the Time Machine may or may not store the files in a flat folder structure. Network backups are stored as a sparse disk image and furthermore rsync doesn't respect all the ACL and permissions that are possible or deal with special permissions on the User folder, user subfolders, Applications and other special cases.

If you can narrow down which files are being copied and confirm your machine directory is not stored in a disk image, rsync might be acceptable in limited circumstances to copy user files that lack special permissions.

In your specific instance - the files are indeed hard linked which will not make any difference to rsync. When you point rsync at a specific instance in time on your backup - it doesn't really matter how many other hard or soft links point at the files you are restoring. The storage system will read the data from the external drive just as if the files were the only copy on the USB drive. That's the magic of hard links - two directory entries point to the same file so that you can't tell when reading the file that it's a link or a file. Only if you query the link count can a program tell, and rsync cares not about the hard link count when reading.

You should be good to go for any restore of files like documents or pictures.

I advise the following:

1. Make a backup of the current state of the machine, this time using Time Machine's Exclusions Option to remove the offending files (e.g ~/Library/*/python) from the backup.
2. Holding down CommandR at the startup chime, boot into OS X Recovery and erase the startup volume using Disk Utility.
3. Cleanly reinstall OS X on the empty volume
4. Once complete, use Setup Assistant (not Migration Assistant!) to restore the Time Machine Backup.

Notes:

• You can only restore complete backups -not incremental. The TM backup mentioned in (1) must be a complete backup.
• Be wary of what you exclude and only exclude what is necessary. For example, excluding the /System folder will prevent you from performing a full restore via Setup Assistant.
• Why not Migration Assistant? It's prone to cause problems when doing a clean restore.
• The Pondini links provided are for Mountain Lion. All the instructions work exactly the same in Mavericks and are completely applicable.