Copilot/fix coherence analysis issues

[toolate28]

This pull request focuses on updating and expanding the documentation and coordination files for the SpiralSafe ecosystem. The changes clarify release plans, parallel session protocols, security notes, and content propagation strategies. They also introduce or update several markdown files to better guide automated agents, document project structure, and ensure consistency across repositories.

Documentation and Coordination Improvements:

• Added and expanded .claude/RELEASE_PLAN.md, .claude/PARALLEL_SESSION_CONTEXT.md, and .claude/CASCADE_TASKS.md to clarify release sequencing, parallel worker protocols, and orchestrator tasks for the SpiralSafe ecosystem. These documents now include structured task lists, clearer schedules, and updated formatting for readability. [1] [2] [3]
• Enhanced .claude/BUILD_ORIENTATION.md, .claude/ORIENTATION.md, and .claude/CONTEXT.md with additional steps, quick checks, and explicit safety constraints for automated agents. [1] [2] [3]

Content Propagation and Cross-Linking:

• Updated .claude/bump/BUMP-20260113-001-ecosystem-unification.md to detail new content propagation phases, cross-linking requirements for all repos, and integration documentation for the isomorphism proof and related assets. [1] [2] [3]

Security and Formatting Enhancements:

• Improved .claude/MCP_SECURITY_NOTES.md with clearer reporting instructions, explicit operating principles, and consistent formatting for Safe Spiral's philosophy and contact information. [1] [2]

Consistency and Minor Fixes:

• Standardized markdown table formatting and section headers across multiple files for improved readability and uniformity. [1] [2] [3]
• Made minor content additions and formatting tweaks to ensure clarity and completeness in documentation. [1] [2] [3]

These updates collectively improve the maintainability, clarity, and operational guidance for both human contributors and automated agents within the SpiralSafe ecosystem.

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Summary

Describe the change in 1-2 sentences.

ATOM Tag

ATOM: ATOM-TYPE-YYYYMMDD-NNN-description

(Generate with: ./scripts/atom-track.sh TYPE "description" "file")

Why

Why this change is needed and what it enables.

What changed

• Files added
• Scripts
• CI workflows

Verification / Testing

• scripts/validate-bump.sh passes locally (if bump.md changed)
• scripts/validate-branch-name.sh tested on example branches (if applicable)
• bash scripts/verify-environment.sh prints ENV OK
• scripts/test-scripts.sh passes (if scripts changed)
• All shell scripts pass shellcheck
• ATOM tag created and logged

Claude Interaction

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• @mentioning Claude in comments for questions or reviews
• Adding labels: claude:review, claude:help, claude:analyze
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• Ask questions: Claude can explain code, suggest improvements, or identify issues

Example commands:

• @claude please review this PR for ATOM compliance
• @claude explain the changes in scripts/atom-track.sh
• @claude check for security issues
• @claude suggest improvements

Notes

This pull request introduces significant improvements and updates to documentation and process files across the repository to clarify project goals, enhance transparency, and streamline parallel and release workflows. The changes focus on expanding build and session orientation guides, updating the release plan for three major packages, and improving the cross-referencing and integration of mathematical proofs and protocols throughout the SpiralSafe ecosystem.

Documentation and Orientation Updates:

• Expanded .claude/BUILD_ORIENTATION.md, .claude/ORIENTATION.md, and .claude/CONTEXT.md with additional steps, safety constraints, verification procedures, and contact information to guide automated build agents and clarify repository constraints. [1] [2] [3] [4]

Release Plan and Package Organization:

• Updated .claude/RELEASE_PLAN.md to detail the purpose, core content, validation steps, and release artifacts for quantum-redstone, HOPE NPCs, and wave-toolkit. Added immediate actions and clarified package exclusions and testing requirements. [1] [2] [3] [4] [5]

Parallel and Cascade Task Protocols:

• Enhanced .claude/CASCADE_TASKS.md and .claude/PARALLEL_SESSION_CONTEXT.md with additional parallel worker tasks, timing schedules, claiming protocols, and expanded session context, including system state, release plan, and mathematical theorem summaries. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]

Cross-Repo Integration and Isomorphism Proofs:

• Updated .claude/bump/BUMP-20260113-001-ecosystem-unification.md to include new tasks for content propagation, cross-linking, and integration documentation across all related repos, with explicit references to isomorphism proofs and protocol examples. [1] [2] [3] [4] [5] [6]

Security and ATOM Trail Improvements:

• Improved .claude/MCP_SECURITY_NOTES.md to clarify disclosure protocols, operating principles, and ATOM trail references, and updated .atom-trail/prs/PR-87-copilot-sub-pr-86.md and .atom-trail/counters/DOC-20260117.count for ATOM tag consistency. [1] [2] [3] [4]

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Project	Deployment	Review	Updated (UTC)
h.and.s	Ready	Preview, Comment	Jan 20, 2026 8:35am

[github-actions]

🏷️ ATOM Tag Auto-Generated

ATOM Tag: ATOM-PR-20260120-001-copilot-fix-coherence-analysis-issues

This tag has been automatically generated and logged to the ATOM trail.

Usage in commits:

git commit -m "ATOM-PR-20260120-001-copilot-fix-coherence-analysis-issues: Your commit message"

View decision history:

cat .atom-trail/decisions/ATOM-PR-20260120-001-copilot-fix-coherence-analysis-issues.json

Framework Alignment Checklist:

• Visible State - Changes are observable and logged
• Clear Intent - Purpose and reasoning documented
• Natural Decomposition - Work breaks at logical boundaries
• Networked Learning - Knowledge transfers to others
• Measurable Delivery - Success criteria defined

---

ATOM tag generated by Safe Spiral automation

[Copilot]

Pull request overview

This pull request focuses on standardizing formatting across historical documentation files in the archive/ directory. The changes primarily convert asterisk-based italic formatting to underscore-based markdown formatting, add blank lines for improved readability, and fix minor formatting inconsistencies in tables and code blocks.

Changes:

• Converted *italic* to _italic_ throughout historical documentation
• Added blank lines after headings and before lists for consistent spacing
• Standardized markdown table formatting with proper column alignment
• Fixed code block formatting and indentation issues

Reviewed changes

Copilot reviewed 120 out of 445 changed files in this pull request and generated 9 comments.

File	Description
archive/historical-docs/*.md	Formatting standardization (italic syntax, spacing, tables)
archive/docs-legacy-20260107/*.md	Formatting standardization matching historical-docs pattern
.claude/last_atom	Updated ATOM tag reference

Comments suppressed due to low confidence (2)

archive/docs-legacy-20260107/PUBLICATION_MANIFEST_v1.0.md:1

• The escaped asterisk in the filename pattern is inconsistent with standard glob syntax. Should be either compass_artifact_*.md or compass-artifact-*.md without escaping.
  archive/docs-legacy-20260107/PUBLICATION_MANIFEST_v1.0.md:1
• The escaped underscores create an awkward pattern. For a signature line placeholder, use either ___________________ (unescaped) or a clearer placeholder like [Signature].

[Copilot]

The YAML list formatting is broken. List items should each be on separate lines with proper indentation. This appears to be a formatting regression that would break YAML parsing.

[Copilot]

The escaped asterisks (\*\*) are incorrect. These should be unescaped glob patterns (**) for proper pattern matching in the deny list.

[Copilot]

The escaped asterisk in the filename pattern is inconsistent with standard glob syntax. Should be either compass_artifact_*.md or compass-artifact-*.md without escaping.

[Copilot]

The escaped underscores create an awkward pattern. For a signature line placeholder, use either ___________________ (unescaped) or a clearer placeholder like [Signature].

[Copilot]

The escaped asterisk in KENL.\* should be unescaped to properly represent a glob pattern: KENL.*.

[Copilot]

Using four backticks instead of three is non-standard markdown. Code blocks should use three backticks.

[Copilot]

Using four backticks instead of three is non-standard markdown. Code blocks should use three backticks.

[Copilot]

Using four backticks instead of three is non-standard markdown. Code blocks should use three backticks.

[Copilot]

Using four backticks instead of three is non-standard markdown. Code blocks should use three backticks.

[Copilot]

Pull request overview

Copilot reviewed 120 out of 445 changed files in this pull request and generated no new comments.