R75 PLAN-RED — Step 1 Audit
Inventory of the worktree against docs/PLAN-RED.md (authorized T0 2026-04-13). Scope: what is already done, what is pending, what will break when Phase 4 KILL runs.
Baseline: worktree E:/AMS/.worktrees/claude/r75-plan-red/ at commit 00e45436 (Phase 1 + Phase 2 WIP imported from main). Total docs/*.md = 253 files.
§1. Phase 2 glue-file inventory
PLAN-RED §NEW FILES lists 14 targets. Status against worktree:
| # | File | Status | Lines | Notes |
|---|---|---|---|---|
| 1 | 0-mutate/index.md |
present, substantial | 72 | Phase 0 accurate (19 tools, α 5-stage, ζ, η). Links at line 27 to ../concepts/constitution.md which does not exist (constitution is at 3-world/physics/constitution.md). |
| 2 | 0-mutate/lifecycle.md |
present, substantial | 364 | Phase 0 accurate (task_create walkthrough, stdio, Zod, 5-stage α). |
| 3 | 1-transport/index.md |
present, substantial | 179 | Phase 0 accurate. Bottom “See also” still points to ../concepts/α-system-core.md (line 179) — needs retargeting. |
| 4 | 2-plugin/index.md |
present, substantial | 149 | Phase 0. Inbound refs at lines 100, 147, 148 point into concepts/ and architecture/middleware.md (KILL) — needs retargeting. |
| 5 | 2-plugin/boot.md |
present, substantial | 232 | Phase 0 accurate (19 tools, stdio first, better-sqlite3, migrations). Two KILL links at lines 230-231. |
| 6 | 2-plugin/database.md |
present, substantial | 262 | Phase 0 accurate (data/colibri.db, WAL, three load-bearing tables, Zod schemas). Mentions AMS 78 tables only as negation at L204 — acceptable. L259-262 link to ../concepts/ (KILL). |
| 7 | 3-world/index.md |
present, substantial | 86 | Phase 0 aware. L27, L28, L45, L46, L57-61, L86 all link into ../concepts/ which is on KILL. Heavy Phase 5 rewrite needed. |
| 8 | 3-world/physics/index.md |
present, substantial | 182 | L175-180 link into ../../concepts/ (KILL). |
| 9 | 3-world/social/index.md |
present, substantial | 173 | L171-172 link to ../concepts/λ-… + ../concepts/ξ-… (KILL). |
| 10 | 3-world/execution/index.md |
present, substantial | 213 | 4 inbound KILL links (per grep). |
| 11 | 4-additions/index.md |
present, substantial | 226 | L222-224 link to ../concepts/ (KILL). |
| 12 | 5-time/index.md |
present, substantial | 230 | L230 links to ../concepts/β-… (KILL). |
| 13 | 5-time/roadmap.md |
present, substantial | 692 | Phase 0 content correct (28 sub-tasks, 9 groups, 6 rounds). |
| 14 | index.md |
present, substantial | 72 | Master hub rebuilt. L32 still cites inventory-r74-2.md (KILL). L60 cites concepts/index.md (KILL). |
Extra glue files present but not in the 14-row table
PLAN-RED Phase 2 said 14 files; the worktree also has these Phase-2-era files:
0-mutate/where-truth-lives.md— 230 lines. Phase 0. Acceptable donor references (L25, L209-211 explicitly labeldata/ams.dbas legacy bootstrap store). L230 links into../concepts/(KILL).2-plugin/middleware.md— 187 lines. Heritage banner intact (lines 1-29 explicitly flag it as donor genealogy + list Phase 0 5-stage α chain correctly). Body below the banner is AMS 6-layer donor doc. Safe to keep under the banner but PLAN-RED ABSORB row 103 says this should become2-plugin/middleware.md— i.e. this IS the target, needs full Phase 0 rewrite OR keep banner-only posture. Still links../concepts/at L184-186.2-plugin/health.md— 61 lines. Phase 0 status-noted but still names donorAMS_LOG_LEVEL(L51, now corrected to COLIBRI_*) and unimplementednpm run dashboard. Thin — needs extending to match PLAN-REDoperations/monitor.md → 2-plugin/health.mdscope.3-world/physics/constitution.md— 925 lines. Phase 0 accurate (s01 7 axioms absorbed). L911-917 “See also” links into../concepts/(KILL).3-world/physics/hardening.md— 369 lines. Phase 0 + deferred plans.3-world/social/surfaces.md— 216 lines. Phase 0.3-world/execution/scale.md— 784 lines. Phase 0-forward. L772-777 link intoconcepts/(KILL, relative paths are even wrong: missing../).5-time/master-flow.md— 301 lines. Phase 0. L147, L177, L255, L271, L292-296 link intohow-it-works/+concepts/(KILL).
Phase 2 files still to be authored
Pending NEW files (0 lines, directories don’t even exist yet):
3-world/physics/laws/— entire subdirectory missing. PLAN-RED ABSORB rows 84-87 requireproof-store.md,consensus.md,state-fork.md,rule-engine.mdhere.3-world/physics/enforcement/— subdirectory missing. Rows 89, 91 requireintegrity.md,governance.md.3-world/social/— needsllm.md(row 81),reputation.md(row 88),identity.md(row 92).3-world/execution/— needstask-pipeline.md(row 79),skill-registry.md(row 82),decision-trail.md(row 83).5-time/— needsround.md+task.md(row 75),phase.md(implicit from row 114-115).2-plugin/— needsmodes.md(row 80).0-mutate/— needspromises.md(row 95).guides/deploy.md,guides/troubleshoot.md,guides/backup.md— ABSORB rows 110, 111, 113. All three already exist (52/71/53 lines). Likely donor-era residue; need Phase 0 rewrite or KILL.
Tally: 14 enumerated NEW targets ⇒ 13 present (some with drift), 1 pending substantive author (0-mutate/promises.md). Beyond the enumerated 14, 12 additional ABSORB-target files still need authoring inside the new World Schema tree.
§2. Phase 3 ABSORB pair status
41 ABSORB rows in PLAN-RED §ABSORB (lines 73-122). For each pair I checked (a) does the old source still exist, (b) does the new target exist with content.
All 41 old source files still exist. Nothing has been git-mv’d yet.
Classified:
2a. content-drift pending reconciliation (both exist, old + new differ) — 11 pairs
| Old | New (exists) | Status |
|---|---|---|
multi-surface-topology.md |
3-world/social/surfaces.md (216L) |
new is substantial; old still alive |
master-flow.md |
5-time/master-flow.md (301L) |
new is substantial; old still alive |
concepts/α-system-core.md |
2-plugin/boot.md (232L) + 2-plugin/index.md (149L) |
boot covers it; α doc still alive |
constraints.md |
3-world/physics/constitution.md (925L) |
new is substantial (s01 absorbed); old still alive |
truth.md |
0-mutate/where-truth-lives.md (230L) |
new is substantial; old still alive |
scenario.md |
0-mutate/lifecycle.md (364L) |
new is substantial; old still alive |
scale.md |
3-world/execution/scale.md (784L) |
new contains old content verbatim + KILL-target concepts/ links (L772-777) |
extensions.md |
5-time/roadmap.md (692L) |
new is substantial; old still alive |
glossary.md |
reference/glossary.md (401L) |
new is substantial; old still alive |
cross-reference.md |
reference/cross-reference.md (246L) |
new is substantial; old still alive |
design-system.md |
reference/design-system.md (339L) |
new is substantial; old still alive |
architecture/database.md |
2-plugin/database.md (262L) |
new is Phase 0; old still alive |
architecture/middleware.md |
2-plugin/middleware.md (187L) |
new = heritage banner + donor body; old still alive with same banner |
architecture/domains.md |
3-world/index.md (86L) |
new is substantial; old still alive |
architecture/execution-axis.md |
3-world/execution/index.md (213L) |
new is substantial; old still alive |
architecture/legitimacy-axis.md |
3-world/physics/index.md (182L) |
new is substantial; old still alive |
security/hardening.md |
3-world/physics/hardening.md (369L) |
new is substantial; old still alive |
operations/monitor.md |
2-plugin/health.md (61L) |
new is THIN (61L vs old rich doc); content still to migrate |
roadmap/R73-R80-plan.md |
5-time/roadmap.md (692L) |
new is substantial; old still alive |
2b. pending-move (old exists, new absent/missing) — ~22 pairs
Target file missing entirely:
pipeline-definition.md→5-time/round.md+5-time/task.md(both missing)concepts/β-task-pipeline.md→3-world/execution/task-pipeline.md(missing)concepts/γ-server-lifecycle.md→2-plugin/modes.md(missing)concepts/δ-model-router.md→3-world/social/llm.md(missing)concepts/ε-skill-registry.md→3-world/execution/skill-registry.md(missing)concepts/ζ-decision-trail.md→3-world/execution/decision-trail.md(missing)concepts/η-proof-store.md→3-world/physics/laws/proof-store.md(dir+file missing)concepts/θ-consensus.md→3-world/physics/laws/consensus.md(dir+file missing)concepts/ι-state-fork.md→3-world/physics/laws/state-fork.md(dir+file missing)concepts/κ-rule-engine.md→3-world/physics/laws/rule-engine.md(dir+file missing)concepts/λ-reputation.md→3-world/social/reputation.md(missing)concepts/μ-integrity-monitor.md→3-world/physics/enforcement/integrity.md(dir+file missing)concepts/ν-integrations.md→4-additions/index.mdpresent (226L) but absorption not done yetconcepts/π-governance.md→3-world/physics/enforcement/governance.md(dir+file missing)concepts/ξ-identity.md→3-world/social/identity.md(missing)promise.md→0-mutate/promises.md(missing)security/auth.md→3-world/physics/hardening.md(exists, needs merge — auth content absorbed separately)operations/deploy.md→guides/deploy.md(exists 52L — likely drift)operations/troubleshooting.md→guides/troubleshoot.md(exists 71L — likely drift)operations/backup.md→guides/backup.md(exists 53L — likely drift)roadmap/phase-0-execution.md→5-time/roadmap.md(exists, absorption merge needed)guides/reading-order.md→index.md(exists, needs verification it covers reading paths)
2c. already-moved (old gone) — 0 pairs
None.
2d. identity-moves (row 116-122: KEPT one copy)
These rows move the file to its own folder (or keep it in place): guides/quick-start.md, guides/self-build-loop.md, guides/write-a-skill.md, guides/agent-bootstrap.md. All still present — no action needed other than verifying content.
guides/agent-handoff-protocol.md → guides/agent-handoff.md requires a rename (file still under old name).
guides/implementation/PHASE-0-EXECUTION-GUIDE.md → guides/implementation/index.md (both present 35L / 150L-ish; superseding rename pending).
§3. Phase 4 KILL file survey
3a. docs/ KILL targets (PLAN-RED §KILL lines 124-189)
Walked all 76 enumerated files. All 76 still exist — zero deletions performed yet.
Grouped:
| Group | Count | Status |
|---|---|---|
how-it-works/ |
9 (README + index + 7 Greek) | All present |
concepts/ KILL subset (index.md, map.md, arbitration.md) |
3 | All present |
architecture/ KILL subset |
11 (component-map, system-overview, gsd-internals, implementation-status, claude-api, obsidian-sync, p2p-layer, router, server-lifecycle, index, data-model) | All present |
colibri-master-context.md |
1 | Present |
reference/ KILL subset |
17 (config, controllers, gsd-engine, greek-vocabulary, repo-structure, api-rest, database-schema, domain-contracts, dsl, dashboard, composition, events, error-codes, security, phoenix-python-reference, cli, index, mcp-tools) | All present (18 listed in count: mcp-tools is KILL while mcp-tools-phase-0 is SEED) |
operations/ KILL subset |
2 (changelog, config-reference) | All present |
comparisons/ |
2 | All present |
developers/ |
3 | All present |
guides/ KILL subset |
18 (quickstart, glossary, greek-letters, obsidian-setup, tutorials/obsidian-sync, tutorials/first-session, tutorials/merkle-audit, tutorials/index, examples/common-workflows, examples/index, implementation/pre-mcp-bootstrap-sequence, implementation/skill-to-task-map, implementation/task-dependency-graph, implementation/phoenix-port-map, implementation/phase-1..5, implementation/kappa-rule-engine, implementation/lambda-reputation, implementation/theta-consensus) | All present |
| Root docs/ | 4 (faq, inventory-r74-2, session-seal-s6, docs/README.md) | All present |
Additionally, the 15 concepts/α–ξ.md files are on the implicit KILL list (ABSORB row moves them into new layers; once absorbed, originals delete). All 15 present.
Total docs/ KILL scope ≈ 91 files. All present, none deleted.
3b. Non-docs/ KILL scope (PLAN-RED lines 253, 283, 302-306, 316)
| Zone | Target | Present count | Action |
|---|---|---|---|
.claude/skills/ams-* (line 283) |
4 stub dirs | 4 present: ams-executor, ams-observability, ams-pm, ams-tier1-chains |
KILL |
data/meta-prompts/ (line 302) |
15 .md (total 19 files including non-.md) | 15 .md present | KILL |
data/projects/ (line 303) |
PLAN-RED says 4 | Directory does not exist in worktree | Already gone |
data/roadmaps/ (line 304) |
~55 .md | 58 .md present (+ JSON deps; 66 total files) | KILL |
data/*.md remaining (line 306) |
~3 stale | data/README.md only (to UPDATE, not KILL) |
None to kill |
temp/rewrite-r74-plan/ (line 316) |
~10 files | Directory does not exist in worktree | Already gone |
| ROOT updates (line 253) | CLAUDE.md, AGENTS.md, README.md, colibri-world-schema.md → docs/world-schema.md |
All present; world-schema.md already present at docs/world-schema.md (both colibri-world-schema.md at root AND docs/world-schema.md coexist) |
UPDATE root 3 + KILL or MOVE root copy |
Non-docs KILL tally: 4 ams-* dirs + 15 meta-prompt .md + 58 roadmap .md = 77 .md files plus some non-md.
3c. Grand KILL total
~91 (docs/) + ~77 (non-docs/) = ~168 .md files pending deletion. PLAN-RED line 340 quotes “~172” — within margin.
§4. Inbound-link survey
Scope: any file in the worktree that will REMAIN after KILL runs, that contains a markdown link into a KILL path.
4a. Root CANON files (will remain)
Confirmed inbound KILL links:
AGENTS.md:156—](docs/concepts/index.md)(KILL)CONTRIBUTING.md:11—](docs/concepts/index.md)(KILL)CONTRIBUTING.md:15—](docs/concepts/index.md)(KILL)CLAUDE.md:55—](docs/multi-surface-topology.md)(ABSORB source — old file will be deleted after Phase 3)CLAUDE.md:94—](docs/pipeline-definition.md)(ABSORB source — old file will be deleted after Phase 3)AGENTS.md:167—](docs/multi-surface-topology.md)(ABSORB source)AGENTS.md:168—](docs/pipeline-definition.md)(ABSORB source)README.md— no broken KILL links detected
4b. docs/ CANON and Phase 2 new glue (will remain)
Grep across the docs tree surfaces 453 matches across 95 files. Of these, the files that will SURVIVE the cleanup and thus need fixing:
High-priority files to fix in Phase 5 / sub-phase 4D (approximate counts of KILL-target links per file):
| File (survives) | KILL links | Worst lines |
|---|---|---|
3-world/index.md |
10 | 27-28, 45-46, 57-61, 86 |
5-time/master-flow.md |
7 | 147, 177, 255, 271, 292-296 |
3-world/physics/constitution.md |
7 | 911-917 |
3-world/physics/index.md |
6 | 175-180 |
3-world/execution/scale.md |
6 | 772-777 |
2-plugin/middleware.md |
4 | 10, 184-186 |
2-plugin/database.md |
4 | 259-262 |
3-world/execution/index.md |
4 | footer block |
4-additions/index.md |
3 | 222-224 |
2-plugin/index.md |
3 | 100, 147-148 |
2-plugin/boot.md |
2 | 230-231 |
3-world/social/index.md |
2 | 171-172 |
0-mutate/index.md |
1 | 27 (also points to non-existent ../concepts/constitution.md — should be ../3-world/physics/constitution.md) |
0-mutate/where-truth-lives.md |
1 | 230 |
1-transport/index.md |
1 | 179 |
5-time/index.md |
1 | 230 |
index.md |
2 | 32 (inventory), 60 (concepts) |
spec/s17-mcp-surface.md, s18-identity.md, s19-governance.md, s15-gsd-contract.md |
1–5 each | footer See-also blocks — SEED files need link sweep |
architecture/decisions/ADR-003-bft-library.md |
1 | footer |
reference/glossary.md |
34 | concept defs — entire “See” footer set |
reference/cross-reference.md |
50 | entire body is reverse index of KILL |
reference/composition.md / controllers.md / database-schema.md / greek-vocabulary.md / gsd-engine.md / phoenix-python-reference.md / security.md |
total 16 | these ARE on KILL so they die with their links |
reference/extractions/* (13 hits across 11 files) |
1–2 each | footer — SEED (49 files), needs link sweep |
guides/first-pr.md, guides/quick-start.md, guides/reading-order.md, guides/write-a-skill.md, guides/agent-bootstrap.md (implicit), guides/implementation/first-7-prs.md, guides/implementation/task-breakdown.md |
total ~35 | SEED — all need link sweep |
4c. High-leverage fix-points
reference/glossary.md(34 KILL links) andreference/cross-reference.md(50 KILL links) together hold 84 of the 453 broken links — retargeting these two files alone removes ~19% of inbound damage.- SEED
spec/andreference/extractions/files hold footer “See also” blocks that point toconcepts/. Total ~25 links across 20+ SEED files; a scripted sweep is best. - PLAN-RED itself contains many KILL paths definitionally (in the KILL table) — these are OK and should be excluded from the sweep.
§5. Content-drift / freshness in Phase 2 files
Deep read of the eight key Phase 2 files. Donor-AMS keyword scan for 78 tables, 484 tools, data/ams.db, 11 middleware:
| File | Occurrences | Flag |
|---|---|---|
0-mutate/index.md |
0 | Clean Phase 0 |
0-mutate/lifecycle.md |
0 | Clean Phase 0 |
0-mutate/where-truth-lives.md |
3 | Acceptable — L25, L209, L211 explicitly label data/ams.db as legacy bootstrap store. Fact-correct. |
2-plugin/boot.md |
0 | Clean Phase 0 |
2-plugin/database.md |
1 | Acceptable — L204 mentions AMS 78 tables as negation (what Colibri does NOT inherit). |
2-plugin/middleware.md |
0 | Heritage banner doc — banner (L1-29) correctly states Phase 0 is 5-stage. Body below (L35-176) is donor 6-layer/11-stack description. This document is the ABSORB target for architecture/middleware.md per PLAN-RED row 103, so the body needs a Phase 0 rewrite OR full replacement in Phase 3. |
2-plugin/health.md |
0 | Thin (61L); no AMS drift but mentions unimplemented npm run dashboard (L30-31). COLIBRI_LOG_LEVEL is correct (L51 explicitly notes donor AMS_LOG_LEVEL is NOT read). |
3-world/index.md |
0 | Phase 0 aware, but 10 KILL links break cleanup |
5-time/master-flow.md |
0 | Phase 0 accurate — but 7 KILL links + links to how-it-works/ which dies |
5-time/roadmap.md |
0 | Phase 0 accurate (28 sub-tasks, 9 groups, 6 rounds, matches CLAUDE.md §9) |
Specific rewrite targets:
2-plugin/middleware.mdL30-176 — entire donor body below banner should be replaced with a short pointer tocolibri-system.md+ ADR-004 + the Phase 0 α chain, OR deleted and replaced by a clean Phase 0 5-stage middleware description.2-plugin/health.md— needs expansion (absorbingoperations/monitor.md) with Phase 0server_healthsemantics (no HTTP endpoint in Phase 0 — it’s an MCP tool; current L10-14GET /api/healthis donor-era).- All “See also” footer blocks in Phase 2 files — rewrite to point into the new World Schema tree.
index.mdL32 citation ofinventory-r74-2.md(KILL) and L60 citation ofconcepts/index.md(KILL).
§6. Orphan docs
Files inside docs/ that are not classified as SEED, ABSORB-source, ABSORB-target, KILL, or NEW in PLAN-RED:
docs/PLAN-RED.md— the plan itself. Meta. Should be preserved or moved todocs/audits/after execution.docs/world-schema.md— the spine (PLAN-RED line 262 sayscolibri-world-schema.mdat root MOVES here; already here). OK as SEED.docs/assets/css/README.md— 1 line PLAN-RED §SEED “assets/*” covers it implicitly. OK.docs/assets/images/colibri-logo.md— 1 line. Same. OK.
Duplicate file risk: colibri-world-schema.md at repo root (31,023 bytes) AND docs/world-schema.md both exist. PLAN-RED row 261-262 says the root one moves into docs/. The root file should be deleted or the docs/ copy is stale — needs disposition decision in Contract step.
All other docs/ files are accounted for.
§7. Summary numbers
| Metric | Current worktree | PLAN-RED target | Delta |
|---|---|---|---|
| docs/ total .md | 253 | ~120 | –133 |
| docs/ SEED | 85 (spec 20 + ADR 7 + agents 4 + extractions 49 + task-prompts 10 — minus 5 unaccounted) | 85 | 0 |
| docs/ NEW glue (from the 14-row table) authored | 13/14 | 14 | –1 |
| docs/ ABSORB pending-move | ~22 | 0 | –22 |
| docs/ ABSORB content-drift to reconcile | ~19 | 0 | –19 |
| docs/ KILL pending deletion | 91 | 0 | –91 |
| Non-docs/ KILL (ams-* + meta-prompts + roadmaps) | 77 | 0 | –77 |
| Inbound KILL links to fix (in surviving files) | ≥453 (conservative; grep hit) | 0 | –453 |
Critical path: the largest blocker is Phase 3 (22 pending git-mv + 19 drift reconciliations + 12 entirely-missing glue targets beyond the 14-row table). Phase 4 can run mechanically once Phase 3 retargets inbound links. Phase 5 must patch CLAUDE.md, AGENTS.md, CONTRIBUTING.md root files (3 confirmed broken links to docs/concepts/). Phase 2 glue is ~90% done by line count but ~50% done by link hygiene.
R75 Step 1 Audit — 2026-04-16 — branch feature/r75-plan-red-execution @ 00e45436. Next: Step 2 Contract.