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I'm trying to remove an application manually by deleting it and any extras using the search function in Finder.

As a backup, I also ran the app through AppCleaner to see if it caught anything as well and I noticed that AppCleaner marked some files (.plist, plist.lockfile, and some actual folders) that no matter what keyword I use won't show up via finder search.

My settings are to search 'My Mac' and have made sure system files are included and used both 'name matches' & 'name contains' but I can't pull up these files. I have already rebuilt the spotlight index and don't know what else to do when a custom search that explicitly includes system files doesn't yield the expected results.

Did finder search change in os 10.9?

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The Spotlight window does not include files treated as system files by default. Try setting "System files" to "are included":

Or use mdfind:

$ mdfind -name tweetbot
/Applications/Tweetbot.app
/Users/lauri/Library/Application Support/CrashReporter/Tweetbot_4C49445B-E14E-51E5-87DC-7CE59AE6A841.plist
/Users/lauri/Library/Containers/com.tapbots.TweetbotMac/Data/Library/Application Support/CrashReporter/Tweetbot_4C49445B-E14E-51E5-87DC-7CE59AE6A841.plist
/Users/lauri/Library/Containers/com.tapbots.TweetbotMac/Data/Library/Application Support/Tweetbot
/Users/lauri/Library/Containers/com.tapbots.TweetbotMac
/Users/lauri/Library/Speech/Speakable Items/Application Speakable Items/Tweetbot
/Users/lauri/Library/SyncedPreferences/com.tapbots.TweetbotMac.plist
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    mdfind finds system files by default? Good to know! – SilverWolf Jan 22 '18 at 16:42

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