What you are describing is mathematically a directed graph and can be represented in Perl as a Graph object using the module Graph. That module also has a number of methods for processing graphs. For instance, one could do a topological sort to establish the hierarchy of dependencies.

use Graph::Directed;
my $g = Graph::Directed->new;   # A directed graph.
        
$g->add_edge(...);
$g->add_vertex(...);
 
$g->vertices(...)
$g->edges(...)

my @ts = $g->topological_sort;
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For modules in particular, check out Module::Dependency for useful methods.