fix(scripts): eliminate phantom git changes from plugin generation

[WilliamBerryiii]

Description

Eliminated phantom git changes that npm run plugin:generate left in the working tree after every run. The root cause was a delete-and-recreate strategy that touched file timestamps and re-wrote identical content, combined with a --index-info stdin call that broke on Windows due to CRLF encoding.

Plugin Generation — Conditional Writes

Introduced Set-ContentIfChanged in CollectionHelpers.psm1 as the single write choke point for all generated files. The function performs an ordinal comparison of proposed content against the existing file and skips the write when identical. Converted all five production write sites in PluginHelpers.psm1 — Write-MarketplaceManifest, New-PluginLink fallback, plugin.json, README.md, and collection YAML — to route through Set-ContentIfChanged.

Added a GeneratedFiles HashSet to Write-PluginDirectory that tracks every output path and returns it in the result object, enabling downstream orphan detection.

Rewrote Repair-PluginSymlinkIndex to parse git ls-files --stage output, detect mode-120000 entries, skip already-correct symlinks, and use per-entry --cacheinfo calls instead of piped --index-info. The piped approach broke on Windows because PowerShell injected CRLF into stdin, corrupting the index update.

Plugin Generation — Orphan Cleanup

Replaced the delete-and-recreate Refresh strategy in Generate-Plugins.ps1 with orphan cleanup. After overwrite-in-place generation completes, files not present in the GeneratedFiles set are removed, followed by a bottom-up empty-directory sweep. All Remove-Item calls gained -ErrorAction Stop for fail-fast behavior.

Post-Processing Scope

Extracted post-processing into a plugin:postprocess script in package.json, scoping markdownlint-cli2 and markdown-table-formatter to plugins/**/*.md and collections/*.md only. This prevented post-processing from modifying unrelated files in the working tree.

Windows Test Compatibility

Separately fixed 14 pre-existing test failures in Invoke-PptxPipeline.Tests.ps1. The tests created shell-script .exe python stubs that are not valid PE executables on Windows. Replaced with .cmd batch files that execute natively and correctly set $LASTEXITCODE.

Test Coverage

• Added a Set-ContentIfChanged test suite in CollectionHelpers.Tests.ps1 covering creation, skip-on-identical, overwrite-on-diff, case-sensitivity, empty string, and UTF-8-without-BOM behavior.
• Added 4 Orphan Cleanup tests in Generate-Plugins.Tests.ps1 validating orphan removal, generated file preservation, empty directory pruning, and DryRun logging.
• Added 5 Repair-PluginSymlinkIndex tests in PluginHelpers.Tests.ps1 using a real git repo fixture — covers DryRun counting, DryRun index immutability, mode-120000 re-indexing, and skip-if-already-fixed logic.

Related Issue(s)

Closes #1029

Type of Change

Select all that apply:

Code & Documentation:

• Bug fix (non-breaking change fixing an issue)
• New feature (non-breaking change adding functionality)
• Breaking change (fix or feature causing existing functionality to change)
• Documentation update

Infrastructure & Configuration:

• GitHub Actions workflow
• Linting configuration (markdown, PowerShell, etc.)
• Security configuration
• DevContainer configuration
• Dependency update

AI Artifacts:

• Reviewed contribution with prompt-builder agent and addressed all feedback
• Copilot instructions (.github/instructions/*.instructions.md)
• Copilot prompt (.github/prompts/*.prompt.md)
• Copilot agent (.github/agents/*.agent.md)
• Copilot skill (.github/skills/*/SKILL.md)

Other:

• Script/automation (.ps1, .sh, .py)
• Other (please describe):

Testing

Full test suite validated after both commits:

• 1707 passed, 0 failed, 1 skipped
• PSScriptAnalyzer clean on all modified PowerShell files
• New tests cover Set-ContentIfChanged, orphan cleanup, and Repair-PluginSymlinkIndex comprehensively

Checklist

Required Checks

• Documentation is updated (if applicable)
• Files follow existing naming conventions
• Changes are backwards compatible (if applicable)
• Tests added for new functionality (if applicable)

AI Artifact Contributions

Required Automated Checks

The following validation commands must pass before merging:

• Markdown linting: npm run lint:md
• Spell checking: npm run spell-check
• Frontmatter validation: npm run lint:frontmatter
• Skill structure validation: npm run validate:skills
• Link validation: npm run lint:md-links (pre-existing failures only — no new broken links introduced)
• PowerShell analysis: npm run lint:ps
• Plugin freshness: npm run plugin:generate

Security Considerations

• This PR does not contain any sensitive or NDA information
• Any new dependencies have been reviewed for security issues
• Security-related scripts follow the principle of least privilege

Additional Notes

• Two test files (CollectionHelpers.Tests.ps1, PluginHelpers.Tests.ps1) gained UTF-8 BOM byte prefix — incidental encoding change from editor saves on Windows, no functional impact.
• No new dependencies introduced. All changes are internal to existing PowerShell modules and npm scripts.

[github-actions]

Dependency Review

✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.

Scanned Files

None

[codecov-commenter]

Codecov Report

❌ Patch coverage is 96.72131% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.84%. Comparing base (52b0885) to head (7348319).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
scripts/collections/Modules/CollectionHelpers.psm1	90.00%	1 Missing ⚠️
scripts/plugins/Modules/PluginHelpers.psm1	96.15%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1035      +/-   ##
==========================================
- Coverage   87.42%   86.84%   -0.59%     
==========================================
  Files          44       30      -14     
  Lines        7803     5358    -2445     
==========================================
- Hits         6822     4653    -2169     
+ Misses        981      705     -276     

Flag	Coverage Δ
pester	86.84% <96.72%> (+0.81%)	⬆️
pytest	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
scripts/plugins/Generate-Plugins.ps1	96.74% <100.00%> (+0.63%)	⬆️
scripts/collections/Modules/CollectionHelpers.psm1	99.31% <90.00%> (-0.69%)	⬇️
scripts/plugins/Modules/PluginHelpers.psm1	93.06% <96.15%> (+16.61%)	⬆️

... and 14 files with indirect coverage changes

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