samples: CrmKernel — retraction-native algebraic kernel demo (internal-facing)

docs/pr-preservation/141-ci-fix-log.md

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+# PR #141 CI fix log
+
+CI-only fix pass applied 2026-04-24 to unblock merge on
+`feat/servicetitan-crm-demo` (PR #141, "samples: CrmKernel —
+retraction-native algebraic kernel demo"). Zero unresolved
+review threads at start; only CI checks were red. No review
+re-drain, no scope change to the PR's substantive diff.
+
+## Pre-fix state
+
+- `mergeStateStatus`: `BLOCKED`.
+- `state`: `OPEN` (branch one commit behind `origin/main`;
+  rebase clean, no conflicts).
+- Check results (per `gh pr checks 141`):
+  - `lint (markdownlint)` — FAIL
+  - `check memory/MEMORY.md paired edit` — FAIL
+  - Everything else green (`build-and-test (ubuntu-22.04)`,
+    `lint (actionlint)`, `lint (no empty dirs)`,
+    `lint (semgrep)`, `lint (shellcheck)`,
+    `lint memory/MEMORY.md reference-existence`,
+    `Path gate`, `Analyze (csharp)`, `Analyze (actions)`,
+    `submit-nuget`).
+
+## Per-failure record
+
+### Failure 1 — `lint (markdownlint)`
+
+**Run:** GitHub Actions run `24902734336`, job
+`72924293173`.
+
+**Violations reported:**
+
+```
+docs/hygiene-history/loop-tick-history.md:175:2974
+  MD056/table-column-count
+  Table column count [Expected: 6; Actual: 4;
+                      Too few cells, row will be missing data]
+docs/hygiene-history/loop-tick-history.md:176:2028
+  MD056/table-column-count
+  Table column count [Expected: 6; Actual: 4;
+                      Too few cells, row will be missing data]
+```
+
+**Root cause:** The tick-history table schema is 6 columns
+(`date | agent | cron-id | action-summary | commit-or-link |
+notes`). The auto-loop-44 and auto-loop-45 rows authored in
+this PR packed `commit-or-link` and `notes` content into the
+`action-summary` mega-cell, leaving only 4 pipe-separated
+fields per row.
+
+**Fix applied:** Split each offending row into the full
+6-column shape. Commit-or-link fields cite pre-tick
+`acb9858` (SignalQuality + /btw landing) for row 175 and the
+PR branch name for row 176; notes fields summarize the
+bilateral-verbatim-anchor discipline (auto-loop-44) and
+speculative-work known-gap-fix tier (auto-loop-45).
+
+Append-only discipline (Otto-229) honoured: no existing
+prior row was edited; the fix is a structural completion of
+rows *introduced by this PR*, not a rewrite of rows
+previously landed on `main`.
+
+**Verification:**
+
+```bash
+npx markdownlint-cli2@0.18.1 "**/*.md"
+# exit=0
+```
+
+### Failure 2 — `check memory/MEMORY.md paired edit`
+
+**Run:** GitHub Actions run `24902734259`, job
+`72924292873`.
+
+**Violations reported:** Five new `memory/**.md` files landed
+on the PR branch without corresponding `memory/MEMORY.md`
+index entries:
+
+- `memory/observed-phenomena/2026-04-19-transcript-duplication-splitbrain-hypothesis.md`
+- `memory/project_aaron_drop_zone_protocol_2026_04_22.md`
+- `memory/project_arc3_adversarial_self_play_emulator_absorption_scoring_2026_04_22.md`
+- `memory/project_operator_input_quality_log_directive_2026_04_22.md`
+- `memory/project_reproducible_stability_as_obvious_purpose_2026_04_22.md`
+
+The NSA-001 canonical incident (see
+`docs/hygiene-history/nsa-test-history.md`) is exactly this
+shape: memory-file-landed-without-pointer is undiscoverable
+by future cold-start sessions.
+
+**Fix applied:** Added five newest-first index entries to
+`memory/MEMORY.md`, inserted immediately after the
+`📌 Fast path` header paragraph. Each entry follows the
+existing one-line-under-~200-chars bolded-description pattern
+with bracketed link, path target, em-dash separator, and
+short prose follow-up describing composition with prior
+memories.
+
+Order of new entries (newest-first within the 2026-04-22
+auto-loop-43/44/45 tick cluster):
+
+1. `observed-phenomena/2026-04-19-transcript-duplication-splitbrain-hypothesis.md`
+2. `project_aaron_drop_zone_protocol_2026_04_22.md`
+3. `project_arc3_adversarial_self_play_emulator_absorption_scoring_2026_04_22.md`
+4. `project_operator_input_quality_log_directive_2026_04_22.md`
+5. `project_reproducible_stability_as_obvious_purpose_2026_04_22.md`
+
+**Verification:** Full-repo markdownlint still clean after
+the MEMORY.md edit (`exit=0`); the
+`paired-edit` check will pass on next CI run because all
+five file paths now appear in MEMORY.md.
+
+## Build gate
+
+`dotnet build -c Release` on the rebased branch:
+
+- First run: FAIL — `Feldera.Bench` SIGSEGV (exit code 139).
+  Known Otto-248 flake; not reproducible across runs.
+- Retry: `0 Warning(s), 0 Error(s)` — PASS.
+
+## Constraints honoured
+
+- Only `.md` files in the PR's diff plus `memory/MEMORY.md`
+  (plus this log, plus the new `docs/pr-preservation/`
+  directory creation) were touched.
+- No new PRs opened.
+- No merge (`gh pr merge`) invoked.
+- No `docs/BACKLOG.md` edits.
+- No symlinks (Otto-244).
+- No review threads touched (0 unresolved before; 0 after).
+- Append-only discipline honoured on tick-history: no
+  previously-landed-on-`main` row was edited; the fix was
+  restricted to structurally-incomplete rows introduced by
+  this PR itself.
+
+## Post-fix expectation
+
+On push:
+
+- `lint (markdownlint)` → PASS
+- `check memory/MEMORY.md paired edit` → PASS
+- `mergeStateStatus` → `CLEAN` (pending CI re-run)
+
+Auto-merge is already armed on this PR per Otto-224
+discipline; CI clearance should flip the state and land the
+merge without manual intervention.
+
+## Follow-up — reference-existence link-path fix
+
+First push surfaced a sibling check that the original two
+failures masked:
+
+- `lint memory/MEMORY.md reference-existence` — FAIL
+  (`observed-phenomena/2026-04-19-transcript-duplication-
+  splitbrain-hypothesis.md -> ... (not found)`).
+
+**Root cause:** `tools/hygiene/audit-memory-references.sh`
+resolves link targets containing `/` as cwd-relative (from
+repo root), not relative to the `memory/` base dir. The
+existing `](docs/research/...)` precedent in MEMORY.md
+demonstrates the convention — slash-paths must resolve from
+repo root. My new link used the bare
+`](observed-phenomena/...)` form which fails that
+resolution.
+
+**Fix applied:** Rewrote the link target to
+`](memory/observed-phenomena/...)` so it resolves from repo
+root like the sibling `docs/research/...` entry. Local audit
+after the fix: 454 refs checked, 454 resolved, 0 broken.
+Commit `b4ff814` pushed on top of the main CI fix commit
+`1cacebe`.
+
+## Rebase pass — 2026-04-24 post-#144 DIRTY clear
+
+PR #144 (Aurora transfer absorb) landed on `main` and
+dirtied this branch. `mergeStateStatus` flipped from `CLEAN`
+back to `DIRTY`; 0 unresolved threads, 0 failing checks —
+pure merge-conflict drain.
+
+**Conflicts resolved** (11 files):
+
+- Append-only / audit-trail files taken from `main` side
+  (`--ours` in rebase semantics) per Otto-229 discipline:
+  `.gitignore`, `docs/AUTONOMOUS-LOOP.md`,
+  `docs/BACKLOG.md`, `docs/force-multiplication-log.md`,
+  `docs/hygiene-history/loop-tick-history.md`,
+  `docs/research/amara-network-health-oracle-rules-stacking-2026-04-22.md`,
+  `drop/README.md`.
+- Code files taken from `main` side as well:
+  `Zeta.sln`, `src/Core/SignalQuality.fs`,
+  `tests/Tests.FSharp/Algebra/SignalQuality.Tests.fs`.
+  Rationale: `SignalQuality.fs` and its tests already
+  landed on `main` via #144 + subsequent review-drain
+  commits (fe156aa, 1ab9351, 44654ec), carrying strict
+  superset improvements — empty-string returns `0.5` +
+  `Pass` severity, NaN weight-poisoning guard in composite
+  math, length-direct read of `MemoryStream` (no
+  `.ToArray()` allocation), weight > 0L filter on grounding
+  / falsifiability predicates, and IP-strip language
+  cleanup. The PR branch carried the pre-drain variant;
+  `main` is strictly ahead.
+- `Zeta.sln`: `main` already has a `ServiceTitanCrm`
+  project entry using the same project GUID
+  (`{D44AB9CA-F491-41F4-96CE-B061238F3D6E}`) the PR's
+  `CrmKernel` entry would have introduced. Taking `main`
+  keeps the non-conflicting `ServiceTitanCrm` entry.
+- `samples/CrmKernel/` directory (added by the PR's first
+  commit) removed via `git rm -rf` — superseded by
+  `samples/ServiceTitanCrm/` which already lives on `main`
+  with the same content modulo the `CrmKernel ->
+  ServiceTitanCrm` rename. Keeping the `CrmKernel`
+  directory would duplicate source at the filesystem level
+  and cause a project-GUID collision in the solution.
+
+**Net result:** The first PR commit (`fee44e4`, the
+substantive `samples: CrmKernel + SignalQuality` patch)
+became empty after resolution and was dropped by
+`git rebase --continue`. The three CI-fix commits
+(`1cacebe`, `b4ff814`, `baaad9d`) rebased cleanly (one
+more tick-history conflict resolved identically with
+`--ours`) and retain their content.
+
+**Build + test after rebase:**
+
+- `dotnet build -c Release` — `0 Warning(s)`, `0 Error(s)`
+  (Build succeeded; 15.26s).
+- `dotnet test Zeta.sln -c Release --no-build` — all four
+  test assemblies pass:
+  - Core.CSharp.Tests: 2 / 2 passed
+  - Bayesian.Tests: 8 / 8 passed
+  - Tests.CSharp: 8 / 8 passed
+  - Tests.FSharp: 694 / 695 passed (1 skipped — the
+    pre-existing `RecursiveCountingMultiSeedTests` skip
+    that is unrelated to this PR)
+
+**Branch state:** 4 commits ahead of origin/main
+(`7b34dc6 ci: fix PR #141 markdownlint MD056 + MEMORY.md
+paired-edit`, `f195804 ci: fix reference-existence path`,
+`20de672 ci: document reference-existence follow-up`, plus
+the rebase-pass log-update commit landing this section).
+`--force-with-lease` push follows. Expect
+`mergeStateStatus` to flip `DIRTY → CLEAN` once refs
+update and CI greens.
+
+**Constraints honoured:** no new PRs opened, no merge
+triggered (auto-merge armed via Otto-224 from the earlier
+open-PR pass), no review-thread edits, build + test gate
+clean, no symlinks introduced.
+
+---
+
+## 2026-04-24T post-rebase review-drain pass (2 new threads)
+
+After the #144 merge + earlier rebase pass, Copilot and
+Codex re-reviewed the branch and raised two new threads
+against `src/Core/SignalQuality.fs`. The file was reverted
+to its pre-fix shape by an earlier cherry-pick sequence
+(the `e206b69` fixes referenced in the resolved threads
+are no longer present in this branch's history), so the
+two new threads are a legitimate re-raise and need the
+fixes re-applied here.
+
+**Thread 1 — P0 (Copilot):** `open System.Runtime.CompilerServices`
+at line 8 is unused; with `TreatWarningsAsErrors` on this
+will fail the build on `FS1182` (unused open).
+**Fix:** removed the unused `open`. The module never
+referenced any symbol from `System.Runtime.CompilerServices`
+(no `[<MethodImpl>]`, no `[<Extension>]` on a module that
+needed it — the extension-style `compressionMeasure`-etc.
+entry points are regular `let`-bound functions).
+
+**Thread 2 — P2 (Codex):** `composite` silently ignores
+negative weights. `sumWeighted <- sumWeighted + w * f.Score`
+with `w = 0.0` and `f.Score = NaN` produces NaN (because
+`0.0 * NaN = NaN`); with negative `w` the dimension
+participates in an inverted direction. Reconcile to one
+consistent rule.
+**Fix:** gated the inner loop on `w > 0.0` and, inside
+that guard, separated the NaN branch (flips `sawNaN`
+without touching the accumulators) from the valid-score
+branch (adds to both `sumWeighted` and `sumWeights`).
+Negative weights and `0.0` weights now explicitly do not
+participate — documented in the docstring as "Weight
+semantics" so callers can see the contract without
+reading code. This matches the documented "missing /
+ignored dimensions contribute 0" behavior and prevents
+silent corruption on misconfigured weight maps.
+
+**Build:** `dotnet build -c Release` → 0 Warning(s)
+0 Error(s).
+
+**Branch state:** push `--force-with-lease` follows.
+Auto-merge armed from prior pass; no new PR opened.
+Constraints preserved (no symlinks, append-only audit
+trail, reply+resolve per thread, role-ref attribution in
+docstring).