Introduce internal-dependencies domain

[JohT]

🚀 Feature

• Introduce internal-dependencies domain
• ⚠️ BREAKING ⚠️ Remove legacy internal dependencies reports and notebooks
• Add --keep-running option to analyze.sh

⚙️ Optimization

• Gracefully stop Neo4j before terminating it
• Add function to check if a projection exists
• Deprecate neovis.js graph visualization notebooks

[Copilot]

Pull request overview

This PR introduces a new internal-dependencies domain under domains/ to generate internal dependency analysis outputs (CSV, SVG charts, GraphViz visualizations, and a Markdown summary report) from Neo4j/GDS data, following the repository’s domain “vertical slice” pattern.

Changes:

• Adds domain entry points for CSV export, Python chart generation, GraphViz visualizations, and Markdown report assembly.
• Adds/copies Cypher query sets for internal dependencies, cyclic dependencies, path finding, and topological sort, plus exploration queries and notebooks.
• Adds a Python chart generator to produce SVGs from path-finding CSV outputs and integrates them into the Markdown summary.

Reviewed changes

Copilot reviewed 60 out of 60 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
domains/internal-dependencies/README.md	Documents the new domain, entry points, structure, prerequisites, and produced outputs.
domains/internal-dependencies/PREREQUISITES.md	Details required upstream pipeline/enrichment steps (Neo4j, weights, projections, TypeScript enrichment, etc.).
domains/internal-dependencies/COPIED_FILES.md	Tracks original→copied file mappings for later deprecation/migration work.
domains/internal-dependencies/internalDependenciesCsv.sh	New CSV pipeline entry point orchestrating internal deps, cycles, path finding, and topological sort into reports/internal-dependencies/.
domains/internal-dependencies/internalDependenciesPython.sh	Runs the Python SVG chart generator for path finding outputs.
domains/internal-dependencies/internalDependenciesVisualization.sh	Entry-point delegator to GraphViz orchestration script.
domains/internal-dependencies/internalDependenciesMarkdown.sh	Entry-point delegator to Markdown summary assembly script.
domains/internal-dependencies/pathFindingCharts.py	Generates SVG charts from path finding CSVs across abstraction levels.
domains/internal-dependencies/graphs/internalDependenciesGraphs.sh	Orchestrates GraphViz visualizations (build levels + longest paths) for Java artifacts, TS modules, and NPM packages.
domains/internal-dependencies/summary/internalDependenciesSummary.sh	Assembles the final Markdown report by running Cypher queries + embedding includes and SVG references.
domains/internal-dependencies/summary/report.template.md	Markdown report template describing interpretation and embedding query/chart/graph outputs.
domains/internal-dependencies/queries/internal-dependencies/Candidates_for_Interface_Segregation.cypher	Cypher: interface segregation candidates table.
domains/internal-dependencies/queries/internal-dependencies/Get_file_distance_as_shortest_contains_path_for_dependencies.cypher	Cypher: reads file-distance distribution from relationship property.
domains/internal-dependencies/queries/internal-dependencies/How_many_classes_compared_to_all_existing_in_the_same_package_are_used_by_dependent_packages_across_different_artifacts.cypher	Cypher: cross-artifact class usage ratios.
domains/internal-dependencies/queries/internal-dependencies/How_many_elements_compared_to_all_existing_are_used_by_dependent_modules_for_Typescript.cypher	Cypher: TS element usage ratios by dependent modules.
domains/internal-dependencies/queries/internal-dependencies/How_many_packages_compared_to_all_existing_are_used_by_dependent_artifacts.cypher	Cypher: artifact package usage ratios.
domains/internal-dependencies/queries/internal-dependencies/Inter_scan_and_project_dependencies_of_Typescript_modules.cypher	Cypher: exploration query for inter-scan/project module deps.
domains/internal-dependencies/queries/internal-dependencies/Java_Artifact_build_levels_for_graphviz.cypher	Cypher: Java artifact edges annotated with build levels for GraphViz.
domains/internal-dependencies/queries/internal-dependencies/List_all_Java_artifacts.cypher	Cypher: artifact listing with dependency counts and sizes.
domains/internal-dependencies/queries/internal-dependencies/List_all_Typescript_modules.cypher	Cypher: TS module listing with dependency counts and element counts.
domains/internal-dependencies/queries/internal-dependencies/List_elements_that_are_used_by_many_different_modules_for_Typescript.cypher	Cypher: widely used TS elements.
domains/internal-dependencies/queries/internal-dependencies/List_types_that_are_used_by_many_different_packages.cypher	Cypher: widely used Java types.
domains/internal-dependencies/queries/internal-dependencies/NPM_Package_build_levels_for_graphviz.cypher	Cypher: NPM package edges annotated with build levels for GraphViz.
domains/internal-dependencies/queries/internal-dependencies/Set_file_distance_as_shortest_contains_path_for_dependencies.cypher	Cypher: computes and writes file-distance property on DEPENDS_ON relationships.
domains/internal-dependencies/queries/internal-dependencies/Typescript_Module_build_levels_for_graphviz.cypher	Cypher: TS module edges annotated with build levels for GraphViz.
domains/internal-dependencies/queries/cyclic-dependencies/Cyclic_Dependencies.cypher	Cypher: Java package cyclic dependency overview.
domains/internal-dependencies/queries/cyclic-dependencies/Cyclic_Dependencies_Breakdown.cypher	Cypher: Java package cyclic dependency breakdown (all edges).
domains/internal-dependencies/queries/cyclic-dependencies/Cyclic_Dependencies_Breakdown_Backward_Only.cypher	Cypher: Java package cyclic dependency backward edges only.
domains/internal-dependencies/queries/cyclic-dependencies/Cyclic_Dependencies_between_Artifacts_as_unwinded_List.cypher	Cypher: cyclic deps between artifacts (edge list).
domains/internal-dependencies/queries/cyclic-dependencies/Cyclic_Dependencies_for_Typescript.cypher	Cypher: TypeScript module cyclic dependency overview.
domains/internal-dependencies/queries/cyclic-dependencies/Cyclic_Dependencies_Breakdown_for_Typescript.cypher	Cypher: TypeScript cyclic dependency breakdown (all edges).
domains/internal-dependencies/queries/cyclic-dependencies/Cyclic_Dependencies_Breakdown_Backward_Only_for_Typescript.cypher	Cypher: TypeScript cyclic dependency backward edges only.
domains/internal-dependencies/queries/path-finding/Path_Finding_1_Create_Projection.cypher	Cypher: example projection creation (exploration).
domains/internal-dependencies/queries/path-finding/Path_Finding_2_Estimate_Memory.cypher	Cypher: example memory estimation (exploration).
domains/internal-dependencies/queries/path-finding/Path_Finding_3_Depth_First_Search_Path.cypher	Cypher: example DFS path query (exploration).
domains/internal-dependencies/queries/path-finding/Path_Finding_4_Breadth_First_Search_Path.cypher	Cypher: example BFS path query (exploration).
domains/internal-dependencies/queries/path-finding/Path_Finding_5_All_pairs_shortest_path_distribution_overall.cypher	Cypher: APSP overall distribution.
domains/internal-dependencies/queries/path-finding/Path_Finding_5_All_pairs_shortest_path_distribution_per_project.cypher	Cypher: APSP distribution per project with examples.
domains/internal-dependencies/queries/path-finding/Path_Finding_5_All_pairs_shortest_path_examples.cypher	Cypher: APSP example paths (top longest shortest paths).
domains/internal-dependencies/queries/path-finding/Path_Finding_6_Longest_paths_distribution_overall.cypher	Cypher: longest path overall distribution.
domains/internal-dependencies/queries/path-finding/Path_Finding_6_Longest_paths_distribution_per_project.cypher	Cypher: longest path distribution per project with examples.
domains/internal-dependencies/queries/path-finding/Path_Finding_6_Longest_paths_examples.cypher	Cypher: example longest paths.
domains/internal-dependencies/queries/path-finding/Path_Finding_6_Longest_paths_for_graphviz.cypher	Cypher: DOT edges for isolated longest paths graph.
domains/internal-dependencies/queries/path-finding/Path_Finding_6_Longest_paths_contributors_for_graphviz.cypher	Cypher: DOT edges highlighting longest-path contributors.
domains/internal-dependencies/queries/path-finding/Set_Parameters.cypher	Cypher Browser :params example for packages.
domains/internal-dependencies/queries/path-finding/Set_Parameters_Typescript_Module.cypher	Cypher Browser :params example for TS modules.
domains/internal-dependencies/queries/path-finding/Set_Parameters_NonDevNpmPackage.cypher	Cypher Browser :params example for NPM non-dev packages.
domains/internal-dependencies/queries/topological-sort/Topological_Sort_Write.cypher	Cypher: writes topological sort properties to nodes.
domains/internal-dependencies/queries/topological-sort/Topological_Sort_Query.cypher	Cypher: queries topological sort properties to CSV.
domains/internal-dependencies/queries/topological-sort/Topological_Sort_List.cypher	Cypher: lists topological sort results and overall levels.
domains/internal-dependencies/queries/topological-sort/Topological_Sort_Exists.cypher	Cypher: checks whether topological sort properties exist.
domains/internal-dependencies/queries/topological-sort/Set_Parameters.cypher	Cypher Browser :params example for topological sort.
domains/internal-dependencies/queries/exploration/Artifacts_with_duplicate_packages.cypher	Exploration query used by notebooks (duplicate packages).
domains/internal-dependencies/queries/exploration/Annotated_code_elements.cypher	Exploration query used by notebooks (annotation usage).
domains/internal-dependencies/explore/InternalDependenciesJava.ipynb	Copied exploration notebook with validation disabled.
domains/internal-dependencies/explore/InternalDependenciesTypescript.ipynb	Copied exploration notebook with validation disabled.
domains/internal-dependencies/explore/PathFindingJava.ipynb	Copied exploration notebook with validation disabled.
domains/internal-dependencies/explore/PathFindingTypescript.ipynb	Copied exploration notebook with validation disabled.
.github/prompts/plan-internal_dependencies_domain.prompt.md	Adds the detailed planning prompt used to create this domain.
.github/prompts/plan-external_dependencies_domain.prompt.md	Updates/introduces the external-dependencies planning prompt reference.

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Pull request overview

Copilot reviewed 66 out of 66 changed files in this pull request and generated 2 comments.

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Copilot reviewed 53 out of 83 changed files in this pull request and generated 3 comments.

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