Improve README.md, fix coverage reports, add Java warning suppression DSL

[alexander-yevsyukov]

This PR updates README.md addressing #56 and #283.

Java renderer settings

• Added JavaValidationRendererSettings proto as the typed envelope for
  settings consumed by JavaValidationRenderer. It carries a
  SuppressWarnings suppress_warnings field.
• Renamed the previous ValidationWarnings proto to SuppressWarnings.
  The unsigned_fields = true flag now suppresses the
  "Unsigned integer types are not supported in Java" warning emitted for
  uint32/uint64 fields constrained by (range), (min), or (max).
  The proto3 default false keeps warnings emitted.
• Added the DSL block on ValidationExtension:

  spine {
      validation {
          java {
              suppressWarnings {
                  unsignedFields.set(true)
              }
          }
      }
  }

  Default: no warnings suppressed.
• ValidationGradlePlugin writes the settings file in
  LaunchSpineCompiler.doFirst, not in afterEvaluate, so that a preceding
  clean task cannot delete the file before the compiler subprocess reads
  the settings directory.
• Settings are written in ProtoJson format instead of ProtoBinary, so an
  explicit false value is preserved on disk (proto3 omits defaults from
  the binary wire format).

Other notable changes

• Fixed generation of coverage reports and addressed Codecov settings
  deprecations.
• Latest config was applied.
• Improved scripts related to agent skills.

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[Copilot]

Pull request overview

This PR refreshes the repository’s public-facing README (per #56 / #283) and applies a broader config/tooling update across docs, CI, coverage reporting, and agent instructions.

Changes:

• Expanded README.md with a fuller overview, quick-start, and links to spine.io documentation.
• Updated version references to 2.0.0-SNAPSHOT.444 across Gradle + docs dependency artifacts.
• Adjusted CI/docs tooling: JaCoCo aggregation timing, Codecov upload settings, and link-check workflow generalized for docs/ or site/.

Reviewed changes

Copilot reviewed 36 out of 41 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
version.gradle.kts	Bumps published snapshot version.
README.md	Rewrites README with overview, TOC, examples, and spine.io doc links.
docs/dependencies/pom.xml	Updates docs dependency POM version.
docs/dependencies/dependencies.md	Regenerated dependency/license report for new version.
docs/content/docs/validation/user/01-getting-started/adding-to-build.md	Updates plugin version in docs snippet.
docs/content/docs/validation/developer/build-and-release.md	Updates version example in release docs.
CLAUDE.md	Converts to thin wrapper referencing AGENTS.md plus Claude-specific notes.
buildSrc/src/main/kotlin/io/spine/gradle/report/coverage/JacocoConfig.kt	Adjusts JaCoCo aggregation setup and ensures tests run before report tasks.
AGENTS.md	Consolidates universal agent guidance into a single entrypoint.
.idea/misc.xml	IntelliJ project metadata adjustments.
.idea/live-templates/User.xml	Fixes live-template date format pattern.
.idea/live-templates/README.md	Corrects spelling/whitespace in live templates documentation.
.gitignore	Updates ignores for docs preview site artifacts.
.github/workflows/check-links.yml	Generalizes link-check workflow to auto-detect docs/ vs site/ Hugo roots.
.github/workflows/build-on-ubuntu.yml	Updates Codecov upload configuration to point at aggregated JaCoCo XML.
.github/copilot-instructions.md	Adds repo-specific Copilot instruction entrypoint referencing AGENTS.md.
.codecov.yml	Updates Codecov settings (including deprecation-related changes).
.claude/settings.json	Updates Claude Code permissions and hook configuration.
.agents/tasks/setup-cross-tool-agent-instructions.md	Adds task doc describing agent-instruction consolidation work.
.agents/tasks/reject-required-on-empty.md	Removes completed/outdated task plan.
.agents/tasks/prompt-caching-org.md	Adds task doc about org-level prompt caching strategy.
.agents/tasks/issue-175-set-once-timestamp.md	Removes completed/outdated task plan.
.agents/tasks/check-links.md	Removes completed/outdated task plan.
.agents/skills/pre-pr/SKILL.md	Updates pre-PR orchestration guidance and sentinel contract.
.agents/skills/check-links/SKILL.md	Updates check-links skill to support docs/ or site/ layouts.
.agents/scripts/sanitize-source-code.sh	Tweaks hook behavior around jq presence.
.agents/scripts/publish-version-gate.sh	Tweaks hook behavior around jq presence.
.agents/scripts/protect-version-file.sh	Tweaks hook behavior around jq presence.
.agents/scripts/pre-pr-gate.sh	Tweaks hook behavior around jq presence.
.agents/quick-reference-card.md	Updates condensed safety guidance wording.
.agents/project.template.md	Adds template for repo-specific .agents/project.md.
.agents/project.md	Adds .agents/project.md file (currently template content).
.agents/project-overview.md	Removes prior project overview doc.
.agents/memory/reference/cache-warm-window.md	Adds reference memory about cache warm windows.
.agents/memory/reference/anthropic-api-caching.md	Adds reference memory about Anthropic API caching patterns.
.agents/memory/MEMORY.md	Updates memory index to include new entries.
.agents/memory/feedback/copilot-review-request.md	Adds feedback memory about requesting Copilot reviews programmatically.
.agents/jvm-project.md	Adds JVM-wide requirements/checklist doc.
.agents/_TOC.md	Updates TOC links (replacing project overview with JVM requirements).

Files not reviewed (3)

• .idea/live-templates/README.md: Language not supported
• .idea/live-templates/User.xml: Language not supported
• .idea/misc.xml: Language not supported

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Pull request overview

Copilot reviewed 36 out of 41 changed files in this pull request and generated 4 comments.

Files not reviewed (3)

• .idea/live-templates/README.md: Language not supported
• .idea/live-templates/User.xml: Language not supported
• .idea/misc.xml: Language not supported

[codecov]

Codecov Report

❌ Patch coverage is 33.33333% with 12 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (master@dd65da5). Learn more about missing BASE report.

Additional details and impacted files

@@           Coverage Diff            @@
##             master    #313   +/-   ##
========================================
  Coverage          ?   9.53%           
  Complexity        ?      62           
========================================
  Files             ?      82           
  Lines             ?    2034           
  Branches          ?     160           
========================================
  Hits              ?     194           
  Misses            ?    1834           
  Partials          ?       6           

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[Copilot]

Pull request overview

Copilot reviewed 44 out of 51 changed files in this pull request and generated 3 comments.

Files not reviewed (3)

• .idea/live-templates/README.md: Language not supported
• .idea/live-templates/User.xml: Language not supported
• .idea/misc.xml: Language not supported

[alexander-yevsyukov]

@armiol, two commented out blocks in build.gradle.kts files were left intentionally for easy recovery in the next PR.

[Copilot]

Pull request overview

Copilot reviewed 53 out of 60 changed files in this pull request and generated 6 comments.

Files not reviewed (3)

• .idea/live-templates/README.md: Language not supported
• .idea/live-templates/User.xml: Language not supported
• .idea/misc.xml: Language not supported

[Copilot]

Pull request overview

Copilot reviewed 53 out of 60 changed files in this pull request and generated 2 comments.

Files not reviewed (3)

• .idea/live-templates/README.md: Language not supported
• .idea/live-templates/User.xml: Language not supported
• .idea/misc.xml: Language not supported

Comments suppressed due to low confidence (1)

java-settings/src/main/proto/spine/validation/java/java_validation_renderer_settings.proto:64

• The proto message name SuppressWarnings generates a Java class io.spine.tools.validation.settings.SuppressWarnings, which is easy to confuse with (and can shadow) the standard Java @SuppressWarnings annotation when imported. Consider renaming this message to something more specific (e.g. WarningSuppression / JavaWarningSuppression) to avoid import/name collisions for Java consumers of the settings API.