fix(cli-tools): drop aqua based installation of cli-tools as they are now installed by homebrew at runtime#820
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Replaced 4 files (00-working-protocol, 01-intro, 02-design, 03-tracking) with a structured doc hierarchy: Root level: - CLAUDE.md (renamed from 00-working-protocol, file refs updated) - README.md (§1-4: problem, principles, non-goals, landscape + doc index) - DESIGN.md (§5-7: framework, architecture, domain model + test/failure philosophy) - TRACKING.md (build backlog from §19.2, deferred v2 from §20, open questions) - GLOSSARY.md (§21) docs/ subfolder (load per task): - research-agent.md (§10, §11, §19.1) - patch-pipeline.md (§12, §13) - trigger-adapters.md (§8) - artifact-classifier.md (§9) - output-adapters.md (§14) - failure-modes.md (§15) - project-setup.md (§16, §18, §19.3-19.4) - testing-guide.md (§17.2-17.4) No content removed. All concepts, details, and rationale preserved.
… now installed by homebrew at runtime
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