[WIP] Fix duplicate files in repository and update accordingly

[Claude]

• Baseline: inspect repo status and run current tests
• Remove legacy System_Programming_Projects artifacts and references
• Ensure build/test files only reference src/include/tests
• Update documentation and ignore rules accordingly
• Verify build and tests after changes

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[odeliyach]

@copilot The Pull Request currently shows 0 files changed. It seems the changes weren't pushed to the branch. Please execute the plan, commit the file moves/deletions, and push them to this branch."

[Copilot]

@copilot The Pull Request currently shows 0 files changed. It seems the changes weren't pushed to the branch. Please execute the plan, commit the file moves/deletions, and push them ...

Commit 707f9e7 removes the legacy System_Programming_Projects references and updates CI/doc/ignore, but pushing to claude/cleanup-duplicate-files is blocked by repo protections (GH013: protected ref). Please allow the push or apply the commit so the PR reflects the changes.