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Makefile: Use per-tool version files to fix overzealous rebuilds

Patrick Steinhardt requested to merge pks-makefile-per-tool-versions into master

We've recently introduced a new way to track necessary rebuilds for the git and libgit2 targets by using separate git.version and libgit2.version files. This MR does the same for our remaining tools such that they now only get rebuilt in case their version changes. This completely replaces the Makefile.sha256 hack.

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