Are the numbers for mode (e:g 120000 for link, 100644 for file) are arbitrary or is there any reason for choosing that number?
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They are not arbitrary, but they are an artifact from when it was expected that Git would store Unix permissions for its contents.
On Unix, "644" is a common default permission for files. It means that the owner has read-write access, and other users have read-only access. Symbolic links do not have permissions, so "000" is used instead.
One exception -- "755" is used for executable files, and this is how Git stores that information.
Dietrich Epp
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