refactor directories

README.md

deconvolution/d2graph/d2_algorithms.py

deconvolution/d2graph/d2_graph.py

deconvolution/d2graph/d2_path.py

deconvolution/d2graph/d2_reduction.py

deconvolution/d2graph/path_algorithms.py

deconvolution/d2graph/path_optimization.py

deconvolution/debug_disct.py

deconvolution/dgraph/AbstractDGIndex.py

deconvolution/dgraph/__init__.py

deconvolution/dgraph/d_graph.py

deconvolution/dgraph/graph_manipulator.py

deconvolution/main/analyse_d2_tsv.py

deconvolution/main/d2_to_path.py

deconvolution/main/evaluate.py

deconvolution/main/generate_fake_barcode_graph.py

deconvolution/main/generate_fake_molecule_graph.py

deconvolution/main/gexf_converter.py

deconvolution/main/to_d2_graph.py

tests/Index_test.py