Make sort more consistent accross uses and flags

[ariasuni]

Fix #863 Fix #1030

In some cases, files were sorted twice, which in most cases is harmless. But when two files are determined equal, their order is unchanged (because the sort is stable). With --reverse, equal elements order, which wasn’t changed by the sort, were reversed twice (unchanged).

Also, command lines arguments are now sorted by their path.

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I still need to check the xtests to see if anything’s wrong with my changes, and update the tests that needs it.

[micwoj92]

This branch has conflicts that must be resolved