Hi
After upgrading successfully I have made a backup of my site over Ftp. Can I safely remove files in /cache/upgrades/temp folder?
There are 4 folders in there that were created during several attempts to install which probably account for 30,000+ files on the server
Cheers
halooooom
Yes, you can remove them.
You can also remove cache/themes.
You can also remove upload/upgrades.
Why did this is not deleted by default ?
Got error 500 when I click on the upgrade wizard in the admin menu. Renamed the upgrades/temp folder and now It re-work… so the temp folder was my issue…
Is this a permissions issue ?
cache/themes is recreated after you delete it. It is there for performance reasons. It is a feature 
upload/upgrades stays there so you can retry upgrades and have a look at which files were changed. It’s part of normal maintenance to clean it up. It can be done by pressing “delete package” on the upgrades screen.
The only moments when they have to be manually deleted, or when that makes a difference, is after a botched upgrade that leaves an incoherent state behind. But that is unpredictable by definition…