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This might be a dumb question, however I was wondering how does Linux keep track of the file permissions? We know if we do a "ls -l" we can see the file permissions but when I change the file permissions where is this information actually modified? File's content doesn't change there must be a another or central location but I cannot find a reference to read. Thanks!

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That is all part of the data stored in the file system. So, it's stored in the same data structure used to store file names, size and the blocks on the storage device that make up the actual file.

How exactly that memory layout looks – depends on the file system used. But in general permission information about the file is typically stored alongside its basic name/location/extents information.