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I was curious about how to get rid of junk files - temp files, bad links etc - in fedora core (if there are any). Is there any application that can do that, except the manual removal?
"Junk files" - those in /tmp - are automatically removed periodically. No additional application is required. Cache files for applications (like a web browser) are limited and cleaned by the application preferences, since this is a trade-off for performance.
In other words, there's no action you should need to perform to keep the system "clean". Is there a specific issue you have in mind?
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how to keep fedora core 5 clean
