Introduce java domain

[JohT]

🚀 Feature

• Introduce java domain
• ⚠️ Breaking: Remove legacy java reports and notebooks

🛠 Fix

• Fix missing underline in file name
• Note that requires part in cypher header is optional.
• Relax lint check by skipping CHANGELOG and accepting status 0

[Copilot]

Pull request overview

Introduces a new domains/java/ vertical-slice domain to run Java-focused analysis (Cypher → CSV, Python SVG charts, Markdown summary) within the existing pipeline’s domain discovery model.

Changes:

• Added Java domain entry points (*Csv.sh, *Python.sh, *Markdown.sh) plus report templates and assembly script.
• Added Java Cypher query set (enrichment, artifact dependencies, method metrics, code quality, exploration, validation).
• Added domain documentation and tracking (README.md, PREREQUISITES.md, COPIED_FILES.md), plus updated AGENTS.md and added a planning prompt.

Reviewed changes

Copilot reviewed 44 out of 44 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
domains/java/summary/report_no_java_data.template.md	Fallback content when Java data absent.
domains/java/summary/report.template.md	Main Java Markdown report template with include hooks.
domains/java/summary/javaSummary.sh	Assembles Java Markdown report from query outputs + includes.
domains/java/queries/validation/ValidateJavaTypes.cypher	Validation query for presence of Java type/artifact structure.
domains/java/queries/validation/ValidateJavaPackageDependencies.cypher	Validation query for Java package dependencies.
domains/java/queries/validation/ValidateJavaMethods.cypher	Validation query for Java methods presence.
domains/java/queries/validation/ValidateJavaInternalDependencies.cypher	Validation query for internal Java artifact structure.
domains/java/queries/validation/ValidateJavaExternalDependencies.cypher	Validation query for external Java type dependencies.
domains/java/queries/validation/ValidateJavaArtifactDependencies.cypher	Validation query for Java artifact-to-artifact dependencies.
domains/java/queries/method-metrics/Effective_lines_of_method_code_per_type.cypher	Method LOC aggregation per type.
domains/java/queries/method-metrics/Effective_lines_of_method_code_per_package.cypher	Method LOC + complexity aggregation per package.
domains/java/queries/method-metrics/Effective_Method_Line_Count_Distribution.cypher	Distribution of effective method line counts.
domains/java/queries/java-code-quality/Spring_Web_Request_Annotations.cypher	Spring Web endpoint annotation extraction query.
domains/java/queries/java-code-quality/Java_deprecated_element_usage_detailed.cypher	Detailed deprecated element usage query.
domains/java/queries/java-code-quality/Java_deprecated_element_usage.cypher	Summary deprecated element usage query.
domains/java/queries/java-code-quality/Java_Reflection_usage_detailed.cypher	Detailed reflection usage query.
domains/java/queries/java-code-quality/Java_Reflection_usage.cypher	Summary reflection usage query.
domains/java/queries/java-code-quality/JakartaEE_REST_Annotations.cypher	Jakarta EE/JAX-RS endpoint annotation extraction query.
domains/java/queries/java-code-quality/Annotated_code_elements_per_artifact.cypher	Annotated elements breakdown per artifact.
domains/java/queries/java-code-quality/Annotated_code_elements.cypher	Overall annotation usage breakdown.
domains/java/queries/exploration/JakartaEE_REST_Annotations_Nodes.cypher	Exploration query returning raw nodes for REST annotations.
domains/java/queries/exploration/Get_all_declared_and_inherited_methods_of_a_type.cypher	Exploration query for declared + inherited methods.
domains/java/queries/enrichment/Set_number_of_Java_packages_and_types_on_artifacts.cypher	Enrichment: set per-artifact package/type counts.
domains/java/queries/enrichment/Set_maven_artifact_version.cypher	Enrichment: set Maven version on artifacts from POM.
domains/java/queries/enrichment/Remove_external_type_and_annotation_labels.cypher	Enrichment utility to remove external labels.
domains/java/queries/enrichment/Label_external_types_and_annotations.cypher	Enrichment utility to label external types/annotations.
domains/java/queries/artifact-dependencies/Usage_and_spread_of_internal_artifact_dependents.cypher	Internal dependent spread/usage statistics query.
domains/java/queries/artifact-dependencies/Usage_and_spread_of_internal_artifact_dependencies.cypher	Internal dependency spread/usage statistics query.
domains/java/queries/artifact-dependencies/Outgoing_Java_Artifact_Dependencies.cypher	Computes outgoing artifact dependency counts/weights.
domains/java/queries/artifact-dependencies/Most_used_internal_dependencies_acreoss_artifacts.cypher	Internal dependency usage summary across artifacts.
domains/java/queries/artifact-dependencies/Incoming_Java_Artifact_Dependencies.cypher	Computes incoming artifact dependency counts/weights.
domains/java/queries/artifact-dependencies/Artifacts_with_duplicate_packages.cypher	Detects duplicate Java package names across artifacts.
domains/java/queries/artifact-dependencies/Artifacts_with_dependencies_to_other_artifacts.cypher	Lists artifact-to-artifact dependency relationships.
domains/java/javaPython.sh	Domain entry point for Python chart generation.
domains/java/javaMarkdown.sh	Domain entry point delegating to summary assembly.
domains/java/javaCsv.sh	Domain entry point producing Java code quality + method metrics CSVs.
domains/java/javaCharts.py	Python chart generator for Java domain SVG outputs.
domains/java/explore/MethodMetricsJavaExploration.ipynb	Java method-metrics exploration notebook under domain.
domains/java/artifactDependenciesCsv.sh	Domain entry point producing artifact dependency CSVs + enrichment.
domains/java/README.md	Java domain overview and outputs.
domains/java/PREREQUISITES.md	Java domain prerequisite documentation.
domains/java/COPIED_FILES.md	Original→copy mapping for migrated Java assets.
AGENTS.md	Adds java to documented domains list.
.github/prompts/plan-java.prompt.md	Planning prompt documenting intended Java domain work plan.

[Copilot]

Pull request overview

Copilot reviewed 152 out of 153 changed files in this pull request and generated 6 comments.

[Copilot]

Pull request overview

Copilot reviewed 152 out of 153 changed files in this pull request and generated 3 comments.

[Copilot]

Pull request overview

Copilot reviewed 152 out of 153 changed files in this pull request and generated 3 comments.