Move most stdout output to `detail.json`.

src/bin/aphid/args.rs

src/bin/aphid/display_tree_analysis.rs

src/bin/aphid/justify.rs

src/bin/aphid/main.rs

src/config.rs

src/config/check.rs

src/gene_tree.rs

src/gene_tree/topological_analysis.rs

src/gene_tree/triplet.rs

src/genes_forest.rs

src/genes_forest/filter.rs

src/learn.rs

src/lib.rs

src/model/scenarios.rs

src/optim/bfgs.rs

src/output.rs

src/output/detail.rs

src/tree/node_to_leaves.rs