PLAN RED — Nuke & Rebuild docs/ around World Schema v2

Authorization: T0 Human, 2026-04-13. Scope: full nuke & rebuild. Core model: World Schema v3 (colibri-world-schema.md) — the tree from the handwritten sketch + 7-pass 672-file audit. Principle: Documentation follows the mutation lifecycle, not feature inventory. Last updated: 2026-04-13, post Pass 7 (full repo coverage confirmed).

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Diagnosis

224 .md files, 53,550 lines, 3 MB. Assembled from 3 donor projects (AMS execution, CogniMesh intelligence, Phoenix legitimacy) over 74 rounds. The result:

1. No conceptual glue. Each Greek letter is documented independently. No doc explains how a mutation flows through the system end-to-end as a single coherent act.
2. Heritage ballast. 49 extraction files, ~10 heritage reference docs, duplicate guides (two quickstart files), donor-contaminated operational docs — all preserved “for genealogy” but actively confusing any reader.
3. Feature-first, not engine-first. The organizing principle is “here are 15 concepts (α–ξ)” instead of “here is what happens when you call a tool.” A developer looking at the docs sees a museum of concepts, not a machine to build.
4. Redundant views. The same information exists in: concept doc, how-it-works doc, spec, extraction, reference, guide, architecture overview, comparison, FAQ entry, glossary entry, and cross-reference. 10× duplication with 10× drift risk.

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The New Core: World Schema Tree

0-mutate/         ← "what is a mutation" — the single idea everything follows
1-transport/      ← MCP + JSON-RPC wire format + 19 tools
2-plugin/         ← the server: boot, modes, shutdown, middleware
3-world/          ← the runtime model
  physics/        ← legitimacy axis: constitution, laws, enforcement, hardening
  social/         ← agents: identity, reputation, tiers, surfaces, LLM
  execution/      ← execution axis: task pipeline, skills, decision trail
4-additions/      ← ν integrations: git, Obsidian, Claude API, SDK
5-time/           ← session → round → task → master flow → roadmap
spec/             ← KEPT: s01–s19 (the law library, untouched)
decisions/        ← KEPT: ADR-001 through ADR-006 (untouched)
agents/           ← KEPT: sigma, pm, executor, writeback contracts (untouched)
reference/        ← KEPT: extractions/ (heritage archive, read-only)
                     glossary, tools-phase-0
guides/           ← KEPT: quick-start, first-pr, implementation/ (task-prompts)

Every new directory maps to a DEPTH in the World Schema tree. Every doc answers ONE question: “what happens at this layer when a mutation passes through?”

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Triage: KEEP / MOVE / KILL

SEED (keep untouched, they’re clean)

File	Reason
colibri-system.md	Canonical vision, R73
spec/s01–s19 + spec/index.md	The law library — well-written, Phase-tagged
architecture/decisions/ADR-001–006 + README	Architectural decisions — clean
agents/sigma-orchestrator.md	T1 contract
agents/pm-contract.md	T2 contract
agents/executor-contract.md	T3 contract
agents/writeback-protocol.md	Ordering rules
reference/mcp-tools-phase-0.md	Canonical 19-tool surface
reference/extractions/* (49 files)	Heritage archive — Wave 8 banners done
guides/implementation/task-breakdown.md	63-task catalog
guides/implementation/task-prompts/* (10 files)	Agent prompts — clean
guides/implementation/first-7-prs.md	Bootstrap sequence
guides/first-pr.md	Contributor onboarding
_includes/head_custom.html	Jekyll hero injection
assets/*	CSS, JS, images, SVG
_config.yml	Jekyll config

Total SEED: ~85 files (specs + ADRs + agents + extractions + task-prompts + assets)

ABSORB (content moves into new structure, old file deleted)

Old file	→ New location	What survives
pipeline-definition.md	5-time/round.md + 5-time/task.md	Pipeline zoom levels
multi-surface-topology.md	3-world/social/surfaces.md	4-surface topology
master-flow.md	5-time/master-flow.md	15-step flow
concepts/α-system-core.md	2-plugin/boot.md	Boot sequence, middleware
concepts/β-task-pipeline.md	3-world/execution/task-pipeline.md	8-state FSM
concepts/γ-server-lifecycle.md	2-plugin/modes.md	4 modes, shutdown
concepts/δ-model-router.md	3-world/social/llm.md	Scoring, fallback
concepts/ε-skill-registry.md	3-world/execution/skill-registry.md	SKILL.md contract
concepts/ζ-decision-trail.md	3-world/execution/decision-trail.md	Hash chain
concepts/η-proof-store.md	3-world/physics/laws/proof-store.md	Merkle tree
concepts/θ-consensus.md	3-world/physics/laws/consensus.md	BFT quorum
concepts/ι-state-fork.md	3-world/physics/laws/state-fork.md	Fork protocol
concepts/κ-rule-engine.md	3-world/physics/laws/rule-engine.md	DSL, integer math
concepts/λ-reputation.md	3-world/social/reputation.md	5 domains, decay
concepts/μ-integrity-monitor.md	3-world/physics/enforcement/integrity.md	3 detectors
concepts/ν-integrations.md	4-additions/index.md	Integration patterns
concepts/π-governance.md	3-world/physics/enforcement/governance.md	Voting, time-lock
concepts/ξ-identity.md	3-world/social/identity.md	Soul vector, Ed25519
constraints.md	3-world/physics/constitution.md	7 axioms + constraints
truth.md	0-mutate/where-truth-lives.md	SQLite, WAL, single-writer
promise.md	0-mutate/promises.md	6 core promises (cleaned)
scenario.md	0-mutate/lifecycle.md	End-to-end walkthrough
scale.md	3-world/execution/scale.md	Scale patterns
extensions.md	5-time/roadmap.md	Phase map
glossary.md	reference/glossary.md	Terms
cross-reference.md	reference/cross-reference.md	Reverse index
design-system.md	reference/design-system.md	Visual identity
architecture/database.md	2-plugin/database.md	Schema overview
architecture/middleware.md	2-plugin/middleware.md	5-stage α chain
architecture/domains.md	3-world/index.md	Domain map
architecture/execution-axis.md	3-world/execution/index.md	Axis overview
architecture/intelligence-axis.md	absorbed into social/llm + execution/decision-trail
architecture/legitimacy-axis.md	3-world/physics/index.md	Axis overview
security/auth.md	3-world/physics/hardening.md	Auth Phase 1+ plans
security/hardening.md	3-world/physics/hardening.md	Security controls
operations/deploy.md	guides/deploy.md	Deployment
operations/troubleshooting.md	guides/troubleshoot.md	Troubleshooting
operations/monitor.md	2-plugin/health.md	Health checks
operations/backup.md	guides/backup.md	Backup/restore
roadmap/R73-R80-plan.md	5-time/roadmap.md	Round plan
roadmap/phase-0-execution.md	5-time/roadmap.md	Task dispatch
guides/quick-start.md	guides/quick-start.md	KEPT (one copy)
guides/reading-order.md	index.md (rebuilt)	Reading paths
guides/self-build-loop.md	guides/self-build-loop.md	Dogfooding
guides/write-a-skill.md	guides/write-a-skill.md	Skill authoring
guides/agent-bootstrap.md	guides/agent-bootstrap.md	Cold-start prompt
guides/agent-handoff-protocol.md	guides/agent-handoff.md	4-stage handoff
guides/implementation/PHASE-0-EXECUTION-GUIDE.md	guides/implementation/index.md	Entry point

KILL (deleted outright — no useful content not already captured elsewhere)

File/Dir	Reason
how-it-works/ (9 files)	Redundant simplified versions of concept docs
concepts/index.md, concepts/map.md, concepts/arbitration.md	Superseded by world-schema layers
architecture/component-map.md	484-tool donor map, heritage
architecture/system-overview.md	Superseded by colibri-system.md
architecture/gsd-internals.md	Heritage donor GSD, bannerized
architecture/implementation-status.md	Stale status tracker
architecture/claude-api.md	24-controller donor spec, Phase 0.9+
architecture/obsidian-sync.md	Superseded by additions/obsidian
architecture/p2p-layer.md	Phase 3+ spec, premature
architecture/router.md	Superseded by social/llm
architecture/server-lifecycle.md	Superseded by plugin/modes
architecture/index.md	Rebuilt as 3-world/index.md
architecture/data-model.md	Absorbed into plugin/database
colibri-master-context.md	DEPRECATED since R73
reference/config.md	100% heritage (Wave 8 banner)
reference/controllers.md	Heritage donor controllers
reference/gsd-engine.md	Heritage donor GSD
reference/greek-vocabulary.md	Superseded by world-schema layers
reference/repo-structure.md	Will rebuild as part of index
reference/api-rest.md	Donor REST API, not Phase 0
reference/database-schema.md	Donor 78-table schema
reference/domain-contracts.md	Donor domain contracts
reference/dsl.md	Covered by spec/s12
reference/dashboard.md	Donor dashboard, Phase 1+
reference/composition.md	Donor composition layer
reference/events.md	Covered by spec/s02
reference/error-codes.md	Donor error codes
reference/security.md	Absorbed into hardening
reference/phoenix-python-reference.md	Donor Python map
reference/cli.md	Heritage CLI
reference/index.md	Rebuilt
reference/mcp-tools.md	Heritage 484-tool list (mcp-tools-phase-0 kept)
operations/changelog.md	Heritage R1-R18 log
operations/config-reference.md	Heritage AMS_* config
comparisons/ (2 files)	Premature — no code to compare
developers/ (3 files)	Absorbed into guides/
guides/quickstart.md	Duplicate of quick-start.md
guides/glossary.md	Duplicate of glossary.md
guides/greek-letters.md	Superseded by world-schema
guides/obsidian-setup.md	Absorbed into additions/obsidian
guides/tutorials/obsidian-sync.md	Absorbed into additions/obsidian
guides/tutorials/first-session.md	Absorbed into 0-mutate/lifecycle
guides/tutorials/merkle-audit.md	Absorbed into physics/laws/proof-store
guides/tutorials/index.md	Rebuilt
guides/examples/ (2 files)	Absorbed into lifecycle.md
guides/implementation/pre-mcp-bootstrap-sequence.md	Absorbed into guides/agent-bootstrap
guides/implementation/skill-to-task-map.md	Absorbed into guides/implementation/index
guides/implementation/task-dependency-graph.md	Merged into roadmap
guides/implementation/phoenix-port-map.md	Heritage donor map
guides/implementation/phase-1-kappa-rule-engine.md	Premature Phase 1 guide
guides/implementation/phase-2-lambda-reputation.md	Premature Phase 2 guide
guides/implementation/phase-3-theta-consensus.md	Premature Phase 3 guide
guides/implementation/phase-4-complete-legitimacy.md	Premature Phase 4 guide
guides/implementation/phase-5-extensibility.md	Premature Phase 5 guide
guides/implementation/kappa-rule-engine.md	Duplicate of phase-1
guides/implementation/lambda-reputation.md	Duplicate of phase-2
guides/implementation/theta-consensus.md	Duplicate of phase-3
faq.md	Rebuilt from world-schema
inventory-r74-2.md	Superseded by this plan
session-seal-s6.md	Historical seal, move to reference/
docs/README.md	Stale

Total KILL: ~95 files (plus ~40 files absorbed into new structure)

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NEW FILES TO WRITE (the conceptual glue)

These are the docs that DON’T EXIST yet — the missing connective tissue.

#	File	Purpose	Lines est.
1	0-mutate/index.md	The missing doc. What is a mutation? Why is everything a state transition? The philosophical anchor.	~80
2	0-mutate/lifecycle.md	The missing doc. One mutation, start to finish: enter → gate → validate → dispatch → record → prove. Shows EVERY layer the mutation touches.	~200
3	1-transport/index.md	MCP + stdio + 19 tools. How mutations enter the world.	~100
4	2-plugin/index.md	The server: what boots, what stores, what gates.	~80
5	2-plugin/boot.md	6-step boot from α + γ.	~120
6	2-plugin/database.md	data/colibri.db: WAL, single-writer, earned tables.	~100
7	3-world/index.md	The three sub-worlds: physics, social, execution.	~80
8	3-world/physics/index.md	Legitimacy axis overview + constitution.	~120
9	3-world/social/index.md	Agent model overview.	~80
10	3-world/execution/index.md	Execution axis overview.	~80
11	4-additions/index.md	ν pattern: invoke(*context, #contract) → Record.	~100
12	5-time/index.md	Session → round → task.	~80
13	5-time/roadmap.md	Phase 0–8 with World Schema layer activation.	~150
14	index.md	NEW root hub: World Schema tree as navigation.	~120

Total new: ~14 files, ~1,500 lines

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Execution Order

Phase 1: mkdir new structure (0-mutate/, 1-transport/, etc.)
Phase 2: Write 14 new glue files
Phase 3: Move SEED files into new locations
Phase 4: Delete KILL files
Phase 5: Update _config.yml nav if needed
Phase 6: Final structure verification

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Post-Rebuild Stats (estimated)

Metric	Before	After
Total .md files	224	~120
Lines	53,550	~30,000
Unique views of same info	10×	1×
“Where do I start?” answers	6 different docs	1 (0-mutate/index.md)
Heritage files	scattered	quarantined in reference/extractions/
Conceptual glue docs	0	14

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Non-docs/ zones (full E:\AMS root coverage)

The plan above covers docs/ (225 files). The repo has 672 total .md files across 12 zones. Here is the disposition of every zone outside docs/:

ROOT (7 .md files)

File	Action
CLAUDE.md	UPDATE — add World Schema reference, update §9 paths after restructure
AGENTS.md	UPDATE — align reading order with new 0-5 layer structure
README.md	UPDATE — point “Documentation” link to new docs/index.md
CONTRIBUTING.md	KEEP — clean
CODE_OF_CONDUCT.md	KEEP — standard Contributor Covenant
SECURITY.md	KEEP — clean
colibri-world-schema.md	MOVE → docs/world-schema.md (it’s the new spine, belongs in docs/)

.agents/ (257 files)

Zone	Files	Action
.agents/skills/ (22 dirs)	~22 SKILL.md	KEEP — CANON. 10 are Phase 0 active, 12 are heritage/deferred. Add active/deferred markers to skills README.
.agents/skills/ Phase 0 active	10	colibri-pm, colibri-executor, colibri-tier1-chains, colibri-task-management, colibri-audit-proof, colibri-verification, colibri-mcp-server, colibri-docs-check, colibri-docs-sync, colibri-greek-nav
.agents/skills/ heritage/deferred	12	colibri-growth-strategy, colibri-truthing, colibri-audit-review, colibri-context-primer, colibri-cross-reference, colibri-obsidian-sync, colibri-pr-review, colibri-round-close, colibri-skeleton-generator, colibri-status, colibri-writeback, colibri-repo-facing-polish
.agents/spawns/	215	KEEP — HERITAGE session traces. Read-only. Per CLAUDE.md §9.2.
.agents/swarms/colibri-5/	8	KEEP — ACTIVE (not heritage). Reusable 5-agent parallel templates, battle-tested. Reference from 3-world/social/ or 4-additions/.
.agents/swarms/ other	0	—
.agents/archive/	5	KEEP — HERITAGE (mainmother/mother2 era, explicitly superseded). Read-only.
.agents/README.md	1	UPDATE — add active/deferred skill inventory + note that swarms/colibri-5 is active.

Changes to .agents/: README updated with Phase 0 active vs deferred skill split. Swarms/colibri-5 reclassified from HERITAGE to ACTIVE.

.claude/ (28 files)

Zone	Files	Action
.claude/skills/colibri-*	22	KEEP — MIRROR of .agents/skills/. Known divergent (R75 resync planned).
.claude/skills/ams-*	4 stubs	KILL — These are redirect stubs to donor AMS skills that no longer exist. Dead weight.
.claude/skills/README.md	1	UPDATE — remove ams-* references

.github/ (6 files)

File	Action
ISSUE_TEMPLATE/bug_report.md	KEEP
ISSUE_TEMPLATE/feature_request.md	KEEP
PULL_REQUEST_TEMPLATE.md	KEEP
workflows/CONTRACT.md	KEEP — reviewed Pass 7, paths current
workflows/VERIFICATION.md	KEEP — reviewed Pass 7, paths current
workflows/WORKFLOWS_ALIGNMENT.md	KEEP — reviewed Pass 7, confirms all workflow paths active

data/ (79 files)

Zone	Files	Action
data/ams.db	1 (binary)	KEEP — heritage task store, used for writeback during Phase 0 bootstrap
data/meta-prompts/	15	KILL — donor AMS meta-prompt library. 7 Tier-1 phase prompts (INIT→CLOSE) + 7 specialized + README. Handlebars-templated, $AMS_ROOT-coupled, gsd_* tool refs. Fully superseded by .agents/skills/ (10 active skills) + docs/agents/ contracts.
data/projects/	4	KILL — donor AMS project/plan/todos. All stale.
data/roadmaps/	~55	KILL — 8 donor roadmap projects (ams-core-runtime, peer-to-peer/Phoenix, ams-meta-prompting, obsidian-integration, obsidian-control-plane, 3× probe stubs). JSON dependency graphs + Handlebars content files. Many placeholder topics. All superseded by docs/5-time/roadmap.md.
data/README.md	1	UPDATE — reduce to “Heritage AMS donor data. ams.db kept for Phase 0 writeback.”
data/*.md (remaining)	~3	KILL — stale

Total data/ kills: ~74 .md files (preserving only README + ams.db binary).

temp/ (14 files)

Zone	Action
temp/README.md	KEEP
temp/r71/	KEEP — gitignored scratch
temp/rewrite-r74-plan/	KILL — superseded by PLAN-RED
Everything else	KEEP — gitignored scratch, doesn’t matter

Other zones (no action needed)

Zone	Files	Action
projects/README.md	1	KEEP — donor genealogy
assets/	1	KEEP
.vscode/	1	KEEP
.venv-tools/	53	IGNORE — pip vendor, not docs
.planning/	0	IGNORE — empty
.worktrees/	0	IGNORE — generated

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Updated Totals (full repo)

Metric	Before	After
docs/ .md files	225	~120
data/ .md files	79	1 (README)
.claude/ stale stubs	4	0
temp/ superseded plans	~10	1 (README)
Total repo .md	672	~500
Of which HERITAGE (read-only)	scattered	quarantined: .agents/{spawns,swarms,archive} + reference/extractions/
Of which CANON	unclear	clearly marked: docs/0-5 + spec/ + agents/ + .agents/skills/

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PLAN RED — authorized by T0, 2026-04-13. World Schema v3 is the new spine. Full 672-file audit complete (7 passes).