I had what I think was a "system crash" of my 500 GB SSD that was my system disk. I now think it was because a keyboard malfunction was preventing proper boot operations. I have a 2008 MacPro running 10.11(El-Cap). I needed to boot in Recovery Mode and restore from Time Machine. Then the Applications folder was completely empty, leaving me with a rather useless machine. I found the Time Machine files (in the Backups.backupdb folder of an external drive) and one by one have partially repopulated the Applications folder with Finder and a few other apps (including Chrome with which I am doing this) from a older TM section of the backups, since the recent backups appeared empty in /Applicatiosn and /Library/Frameworks. The system disk used to be named SSD_1 and that's how it appears on my backup displayed in Time Machine, but it currently appears as "Macintosh HD2" in Finder. This which used to be the location of my Time Machine image before installing the SSD. There's also the old Macintosh HD displayed in the Devices side panel, which when you look at it with Get Info appears as "Macintosh HD 1". I'm a bit worried that a clean system install will trash all my applications. I'm also concerned that my "past end of life" machine won't get the right OS files from the Apple servers.
Ideas: 1) Use Get Info on the SSD to rename the startup SSD as "SSD_1" so that it matches the entry in the Time Machine backup files. Then
<somehow> "bless" that drive to use archaic Mac terminology.
2) Or should I clean reinstall. Not even sure I can. Would need to do it over the network and this box is past Apple's end of life rules. This was originally a Lion machine IIRC. I'm not sure what the latest physical medium that holds a DVD image and my DVD door is stuck in the closed position anyway.
Update: As I use Time Machine more to see what's missing, I'm now seeing my old applications and contents of the Frameworks folder at least in the TimeMachine folders (but not on the "real" disk) . So apparently I was not waiting long enough to see the folder display get updated? Can I now use Finder and right-click/GetInfo to rename the SSD to it's old name and then restore from Time Machine? And how does MacOS determine the boot drive?
Eventually, I ended up buying a new Apple-branded keyboard and the system all came back as it used to be, except for renaming the SSD device. The answer below is correct in suggesting I make a recovery disk.