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Transform many package related facts to use a nested function
Each fact that is deduced from package rules, and start with a bare package atom, is transformed into a "facts" atom containing a nested function. For instance we transformed version_declared(Package, ...) -> facts(Package, version_declared(...)) This allows us to clearly mark facts that represent a rule on the package, and will be of help later when we'll have to distinguish the cases where the atom "Package" is being used referred to package rules and not to a node in the DAG.
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