Archive SpecHO repository and clean up codebase

[johnzfitch]

This commit retires the SpecHO project into a clean, archived state:

Cleanup

• Remove log/output files (test_results.log, diagnostic_output.txt, etc.)
• Remove backup files (CLAUDE-old.old.md.bak)
• Remove duplicate SPECS.md from specHO/ module
• Fix hardcoded paths in scripts/manual_analysis.py

Reorganization

• Move debug scripts to docs/archive/experiments/
• Move proposal docs to docs/archive/
• Move sample files to data/samples/
• Update archive INDEX.md with new structure

Documentation

• Rewrite README.md with project evolution story
• Document the counterintuitive finding about human predictability
• Add clear archive notice and final state summary
• Update STATUS.md to reflect archived state

The project achieved its research objectives:

• 32/32 tasks complete, 830 tests passing
• Working 5-component detection pipeline
• Key insight: humans are more fingerprintable than LLMs

[Copilot]

Pull request overview

This PR archives the SpecHO project by cleaning up the codebase and documenting its final state. The project successfully completed all 32 tasks with 830 passing tests and achieved its research objective of demonstrating LLM fingerprinting capabilities. The key counterintuitive finding: human writing is more predictable and fingerprintable than LLM output.

Changes:

• Removed temporary files (logs, outputs, backups, duplicate documentation)
• Fixed hardcoded paths in scripts/manual_analysis.py for cross-platform compatibility
• Reorganized historical materials into docs/archive/experiments/
• Updated documentation to reflect archived status and document research findings

Reviewed changes

Copilot reviewed 13 out of 29 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
test_sample_human.txt	Removed temporary test sample file
test_results.log	Removed test output log (926 lines)
specho-commands.txt	Removed CLI usage guide (archived in docs)
specHO/SPECS.md	Removed duplicate specs (main version in docs/)
scripts/manual_analysis.py	Fixed hardcoded paths to use relative paths
pipeline_output.txt	Removed demo output file
full_test_metrics.txt	Removed test metrics snapshot
fields.txt/fields.json	Removed temporary debugging files
diagnostic_output.txt	Removed diagnostic output file
cli_test_output.txt	Removed CLI test output
CLAUDE-old.old.md.bak	Removed backup file
docs/archive/experiments/*.py	Added debug scripts to archive
docs/archive/*.md	Added proposal/status docs to archive
docs/archive/INDEX.md	Updated with experiments/ section
docs/archive/COMMIT_MESSAGE.txt	Added git commit template
docs/STATUS.md	Updated with archive notice
data/samples/.txt/.md	Moved sample files to data/samples/
README.md	Rewrote with project evolution and archive notice

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