chore: daily update 2026-09-17

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@@ -3,28 +3,30 @@ type: "Reference"
title: "Git repo — evidence index (Obsidian vault + OpenWiki wiki, Robin)"
description: >
Compact manifest of Robin's Obsidian vault + the local OpenWiki wiki, ingested
through the local git-repo connector. **Latest fetch (2026-09-13T18:08Z — 31st
through the local git-repo connector. **Latest fetch (2026-09-16T18:18Z — 32nd
git-repo-1 fetch since 2026-08-07): vault HEAD unchanged at `09bec367` for the
2nd consecutive fetch after the Tomas 2026 + Vijakumaran 2026 resumption; wiki
HEAD bumped `55d930f` → `5f33bd3` via 4 new automated wiki commits (`7cfb801`
sources-sync 2026-09-12 — the **twenty-ninth** consecutive sources-sync +
`999a37d` daily update 2026-09-12 + `0447186` daily update 2026-09-13 +
`5f33bd3` sources-sync 2026-09-13 — the **thirtieth** consecutive sources-sync);
1 working-tree modification at `MOCs/MOC-类器官与3D培养.md` (mtime 2026-09-13
11:55:42 +0800); 8-dirty-file baseline (down from 10-dirty at the 2026-09-11
fetch); carry-forward bump 30/25/25/18 → 32/27/27/20-day.** Two configured
repos: obsidian-vault at /home/ldw/workspace (main branch, HEAD `09bec367`,
2026-09-11, vault silence streak BROKEN after 11 calendar days with 2 new
commits — Tomas 2026 HGSC + Vijakumaran 2026 brain-organoid ALI oxygen
engineering, the first v4 Flywheel auto-sink pipeline entry); and openwiki-wiki
at /home/ldw/.openwiki/wiki (main branch, HEAD `5f33bd3`, 2026-09-13,
bumped from `55d930f` via 4 automated commits in the 48-hour window —
`7cfb801` sources-sync twenty-ninth + `999a37d` daily update + `0447186`
daily update + `5f33bd3` sources-sync thirtieth). This page is a navigation
index — content ingestion (paper deep reads, sales scripts, customer files)
happens via the Hermes skill and RAGFlow, not here.
tags: [sources, git-repo, vault, wiki, manifest, 2026-09-11, 2026-09-10, 2026-09-09, 2026-09-08, 2026-09-07, 2026-09-06, 2026-09-05, 2026-09-04, 2026-09-03, 2026-09-02, 2026-09-01, 2026-08-31, vault-silence-broken, vault-resumed-after-11d, twenty-seventh-sources-sync, twenty-eighth-sources-sync, twenty-ninth-git-repo-fetch, tomas-2026-hgsoc-parpi-spheroid-organoid, vijakumaran-2026-brain-organoid-ali-oxygen-engineering, flywheel-v4-auto-sink, wiki-4-new-commits, review-templates-celvivo-commercial-confirmed-one-off, deepread-40240593-eighteen-silent-fetches]
timestamp: 2026-09-13T18:08:00Z
5th consecutive fetch after the Tomas 2026 + Vijakumaran 2026 resumption; wiki
HEAD bumped `5f33bd3` → `ac46732` via 6 new automated wiki commits (`667730f`
daily update 2026-09-14 + `09f47d6` sources-sync 2026-09-14 — the **thirty-first**
consecutive sources-sync + `f38cebf` daily update 2026-09-15 + `f5465f9`
sources-sync 2026-09-15 — the **thirty-second** consecutive sources-sync +
`73dae5e` daily update 2026-09-16 + `ac46732` sources-sync 2026-09-16 — the
**thirty-third** consecutive sources-sync); 1 working-tree modification at
`MOCs/MOC-类器官与3D培养.md` (mtime 2026-09-13 11:55:42 +0800 — persists
uncommitted for 3 calendar days at this fetch); 11-dirty-file baseline (up from
8-dirty at the 2026-09-13 fetch); carry-forward bump 32/27/27/20 → 35/30/30/23-day.**
Two configured repos: obsidian-vault at /home/ldw/workspace (main branch, HEAD
`09bec367`, 2026-09-11, vault HEAD unchanged at `09bec367` for the 5th consecutive
fetch after the Tomas 2026 + Vijakumaran 2026 resumption; the MOC working-tree
modification persists uncommitted); and openwiki-wiki at /home/ldw/.openwiki/wiki
(main branch, HEAD `ac46732`, 2026-09-16, bumped from `5f33bd3` via 6 automated
commits in the 72-hour window — `667730f` daily update + `09f47d6` sources-sync
thirty-first + `f38cebf` daily update + `f5465f9` sources-sync thirty-second +
`73dae5e` daily update + `ac46732` sources-sync thirty-third). This page is a
navigation index — content ingestion (paper deep reads, sales scripts, customer
files) happens via the Hermes skill and RAGFlow, not here.
tags: [sources, git-repo, vault, wiki, manifest, 2026-09-11, 2026-09-10, 2026-09-09, 2026-09-08, 2026-09-07, 2026-09-06, 2026-09-05, 2026-09-04, 2026-09-03, 2026-09-02, 2026-09-01, 2026-08-31, vault-silence-broken, vault-resumed-after-11d, twenty-seventh-sources-sync, twenty-eighth-sources-sync, twenty-ninth-sources-sync, thirtieth-sources-sync, thirty-first-sources-sync, thirty-second-sources-sync, thirty-third-sources-sync, thirty-second-git-repo-fetch, tomas-2026-hgsoc-parpi-spheroid-organoid, vijakumaran-2026-brain-organoid-ali-oxygen-engineering, flywheel-v4-auto-sink, wiki-6-new-commits, review-templates-celvivo-commercial-confirmed-one-off, deepread-40240593-twenty-two-silent-fetches, deepread-40240593-twenty-three-silent-fetches, vault-silent-5d, vault-silent-6d, vault-silent-7d, moc-organoid-3d-culture-uncommitted-edit-3d, vault-working-tree-moc-modification-2026-09-13-persists, thirty-second-git-repo-fetch-32nd]
timestamp: 2026-09-16T18:18:00Z
---
# Git repo — evidence index
@@ -35,28 +37,28 @@ This page is the **compact source-evidence index** for the local git-repo connec
- Connector config path: `~/.openwiki/connectors/git-repo/config.json`
- Two configured local repos:
- `obsidian-vault` at `/home/ldw/workspace` (branch: `main`, HEAD `09bec36702cdbd8ef1d2644919ca337248ae6bff`, 2026-09-11 — **37 commits since 2026-08-03 fetch**, +2 since 2026-09-09T18:11Z fetch)
- `openwiki-wiki` at `/home/ldw/.openwiki/wiki` (branch: `main`, HEAD `5f33bd3`, 2026-09-13 — bumped from `55d930f` via 4 automated commits in the 48-hour window)
- `obsidian-vault` at `/home/ldw/workspace` (branch: `main`, HEAD `09bec36702cdbd8ef1d2644919ca337248ae6bff`, 2026-09-11 — **37 commits since 2026-08-03 fetch**, +2 since 2026-09-09T18:11Z fetch; vault HEAD unchanged for the 5th consecutive git-repo-1 fetch since the 2026-09-11T18:14Z resumption)
- `openwiki-wiki` at `/home/ldw/.openwiki/wiki` (branch: `main`, HEAD `ac46732ddf9bfe79ea480f1927450073bfd0d893`, 2026-09-16 — bumped from `5f33bd3015e3ac6b740702d55888ba93fe024eab` via 6 automated commits in the 72-hour window)
- Authentication: local path only — no remote, no credentials
## Latest manifest
- `~/.openwiki/connectors/git-repo/raw/2026-09-13T18-08-...-...Z/manifest.json` (generated 2026-09-13T18:08Z — **31st git-repo-1 fetch since 2026-08-07**)
- Vault HEAD: `09bec36702cdbd8ef1d2644919ca337248ae6bff` (**unchanged at `09bec367` for the 2nd consecutive fetch** after the 2026-09-11T18:14Z bump from `391e4713`)
- Wiki HEAD: `5f33bd3` (bumped from `55d930f` via 4 automated commits in the 48-hour window)
- **0 new vault commits** in the 48-hour window + **1 working-tree modification** at `M "04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md"` (mtime 2026-09-13 11:55:42 +0800; Robin actively editing MOC index file but has not yet committed)
- **4 new automated wiki commits** in the 48-hour window (`7cfb801` sources-sync 2026-09-12 — the **twenty-ninth** consecutive sources-sync + `999a37d` daily update 2026-09-12 + `0447186` daily update 2026-09-13 + `5f33bd3` sources-sync 2026-09-13 — the **thirtieth** consecutive sources-sync)
- **8 uncommitted wiki files** in working tree per the manifest `changedFiles` list (down from the prior 10-dirty baseline — `M .last-update.json` + `M sources/hackernews.md` + `M sources/nocodb.md` + `M sources/openwiki-version-drift.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md`)
- **Carry-forward untracked-file bumps**: `Review/zhou2023_computer_vision_microfluidics.md` 30 → **32-day** (28 → **30 fetches silent**), `celvivo_commercial/` + `templates/` 25 → **27-day**, `deepread_40240593/` 18 → **20-day** (mtime unchanged across **19 consecutive silent fetches** since creation)
- `~/.openwiki/connectors/git-repo/raw/2026-09-16T18-18-42-033Z/manifest.json` (generated 2026-09-16T18:18Z — **32nd git-repo-1 fetch since 2026-08-07**)
- Vault HEAD: `09bec36702cdbd8ef1d2644919ca337248ae6bff` (**unchanged at `09bec367` for the 5th consecutive fetch** after the 2026-09-11T18:14Z bump from `391e4713`; **5 calendar days of vault silence** since the 2026-09-11 resumption)
- Wiki HEAD: `ac46732ddf9bfe79ea480f1927450073bfd0d893` (bumped from `5f33bd3` via 6 automated commits in the 72-hour window)
- **0 new vault commits** in the 72-hour window + **1 working-tree modification** at `M "04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md"` (mtime 2026-09-13 11:55:42 +0800; Robin actively editing MOC index file but has not yet committed — the modification now persists uncommitted for **3 calendar days** at this fetch)
- **6 new automated wiki commits** in the 72-hour window (`667730f` daily update 2026-09-14 + `09f47d6` sources-sync 2026-09-14 — the **thirty-first** consecutive sources-sync + `f38cebf` daily update 2026-09-15 + `f5465f9` sources-sync 2026-09-15 — the **thirty-second** consecutive sources-sync + `73dae5e` daily update 2026-09-16 + `ac46732` sources-sync 2026-09-16 — the **thirty-third** consecutive sources-sync)
- **11 uncommitted wiki files** in working tree per the manifest `changedFiles` list (up from the 8-dirty baseline at the 2026-09-13T18:08Z fetch — `M .last-update.json` + `M index.md` + `M quickstart.md` + `M sources/README.md` + `M sources/hackernews.md` + `M sources/nocodb.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md` + `M themes.md`; the 3 daily-update cycles on 2026-09-14 + 2026-09-15 + 2026-09-16 re-touched the synthesis-layer files while the 3 sources-syncs re-touched the 4 source-sync files)
- **Carry-forward untracked-file bumps**: `Review/zhou2023_computer_vision_microfluidics.md` 32 → **35-day** (30 → **33 fetches silent**), `celvivo_commercial/` + `templates/` 27 → **30-day**, `deepread_40240593/` 20 → **23-day** (mtime unchanged across **22 consecutive silent fetches** since creation)
## Carry-forward untracked directories
| Directory / file | Carry-forward | Fetches silent | Status |
| --- | ---: | ---: | --- |
| `Review/zhou2023_computer_vision_microfluidics.md` | **32-day** | 30 | stale carry-forward note (confirmed one-off at 2026-08-27 fetch, demoted at 2026-08-28 fetch) |
| `celvivo_commercial/` | **27-day** | 27 | stale carry-forward note (confirmed one-off alongside `Review/` at 2026-08-28 fetch) |
| `templates/` | **27-day** | 27 | stale carry-forward note (confirmed one-off alongside `Review/` at 2026-08-28 fetch) |
| `deepread_40240593/` | **20-day** | 19 | working-folder pipeline hypothesis continuing to weaken (mtime unchanged across 19 consecutive silent fetches since creation) |
| `Review/zhou2023_computer_vision_microfluidics.md` | **35-day** | 33 | stale carry-forward note (confirmed one-off at 2026-08-27 fetch, demoted at 2026-08-28 fetch) |
| `celvivo_commercial/` | **30-day** | 30 | stale carry-forward note (confirmed one-off alongside `Review/` at 2026-08-28 fetch) |
| `templates/` | **30-day** | 30 | stale carry-forward note (confirmed one-off alongside `Review/` at 2026-08-28 fetch) |
| `deepread_40240593/` | **23-day** | 22 | working-folder pipeline hypothesis continuing to weaken (mtime unchanged across 22 consecutive silent fetches since creation) |
## Robin 8-07 added — untracked regional agent files (context only)
@@ -85,13 +87,29 @@ The 5 most recent vault commits are the new 2 (Tomas 2026 + Vijakumaran 2026) on
6. `030f31ed` 2026-08-31 — deep-read: Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ClinoReactor)
7. `eb24ab72` 2026-08-31 — deep-read: Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids (CelVivo)
## Recent commits — wiki (last 5)
## Recent commits — wiki (last 6)
1. `5f33bd3` 2026-09-13 — chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-09-13, **thirtieth** consecutive sources-sync)
2. `0447186` 2026-09-13 — chore: daily update 2026-09-13 (8 files modified per `git show --stat 0447186`)
3. `999a37d` 2026-09-12 — chore: daily update 2026-09-12 (16 files modified per `git show --stat 999a37d`)
4. `7cfb801` 2026-09-12 — chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-09-12, **twenty-ninth** consecutive sources-sync)
5. `55d930f` 2026-09-11 — chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-09-11, **twenty-eighth** consecutive sources-sync)
1. `ac46732` 2026-09-16 — chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-09-16, **thirty-third** consecutive sources-sync)
2. `73dae5e` 2026-09-16 — chore: daily update 2026-09-16 (per `git show --stat 73dae5e` the commit re-touched the same source-sync files)
3. `f5465f9` 2026-09-15 — chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-09-15, **thirty-second** consecutive sources-sync)
4. `f38cebf` 2026-09-15 — chore: daily update 2026-09-15 (per `git show --stat f38cebf` the commit re-touched the same source-sync files)
5. `09f47d6` 2026-09-14 — chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-09-14, **thirty-first** consecutive sources-sync)
6. `667730f` 2026-09-14 — chore: daily update 2026-09-14 (per `git show --stat 667730f` the commit re-touched the same source-sync files)
7. `5f33bd3` 2026-09-13 — chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-09-13, **thirtieth** consecutive sources-sync)
## Synthesis-policy — this run (2026-09-16T18:18Z)
- **Vault delta: 0 new vault commits + 1 working-tree modification persisting** — vault HEAD unchanged at `09bec367` for the **5th consecutive fetch** after the Tomas 2026 + Vijakumaran 2026 resumption on 2026-09-11T18:14Z. **5 calendar days of vault silence** since the 2026-09-11 resumption. The same MOC-file modification that surfaced at the 2026-09-13T18:08Z fetch (`M "04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md"`, mtime 2026-09-13 11:55:42 +0800) **persists uncommitted for 3 calendar days** at this fetch — Robin is editing the MOC index file but the modification has not been promoted to a commit. No new vault mtime changes were observed in the 2026-09-13T18:08Z → 2026-09-16T18:18Z 72-hour window. The 8 untracked regional agent files from 2026-08-07 carry forward unchanged.
- **Wiki delta: automated maintenance only** (3 daily updates + 3 sources-syncs). The 6 new wiki commits in the 72-hour window are routine: `667730f` daily update 2026-09-14 + `09f47d6` sources-sync 2026-09-14 thirty-first + `f38cebf` daily update 2026-09-15 + `f5465f9` sources-sync 2026-09-15 thirty-second + `73dae5e` daily update 2026-09-16 + `ac46732` sources-sync 2026-09-16 thirty-third. The wiki HEAD bump `5f33bd3` → `ac46732` covers 3 calendar days.
- **Dirty-file baseline change**: 8-dirty baseline (at 2026-09-13T18:08Z) → **11-dirty baseline** (at 2026-09-16T18:18Z). The 3 daily-update cycles re-touched `index.md` + `quickstart.md` + `themes.md` (the 2026-09-13 daily update had cleared them); the 3 sources-syncs re-touched the 4 source-sync files (`sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md`) each cycle. The 11-dirty-file list at 2026-09-16T18:18Z: `M .last-update.json` + `M index.md` + `M quickstart.md` + `M sources/README.md` + `M sources/hackernews.md` + `M sources/nocodb.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md` + `M themes.md`.
- **Carry-forward bump** to **35/30/30/23-day** at this fetch (highest carry-forward durations of the 2026-08-07 streak): `Review/zhou2023_computer_vision_microfluidics.md` 32 → **35-day** (33 fetches silent), `celvivo_commercial/` + `templates/` 27 → **30-day** (30 fetches silent each), `deepread_40240593/` 20 → **23-day** (22 consecutive silent fetches since creation; mtime unchanged at 2026-08-24 16:31 +0800).
- **Synthesis-layer impact**: **none** — vault delta is empty (no new commits, no new mtime changes) and the wiki delta is automated maintenance only. The MOC-file working-tree modification persists uncommitted for 3 calendar days; it does not affect synthesis-layer pages until the commit lands. No `/themes.md` row, no `/commitments.md` row, no `/open-questions.md` row, no `/personal-logistics.md` item is added at this fetch.
- **`/quickstart.md`** gets a new "Latest update — git-repo-1 (2026-09-16T18:18Z)" paragraph + the description frontmatter mentions the 2026-09-16T18:18Z git-repo-1 fetch + the **32nd git-repo-1 fetch** of the 2026-08-07 streak + the **vault-silent-for-5th-consecutive-fetch** event + the 6 new wiki commits (31st/32nd/33rd sources-sync sequence) + the 35/30/30/23-day carry-forward bump + the 11-dirty-file baseline + the MOC-file working-tree modification persisting uncommitted for 3 calendar days
- **`/sources/git-repo.md`** (this page) — description frontmatter refreshed to mention the 2026-09-16T18:18Z fetch; tags refreshed to add `2026-09-16`, `2026-09-15`, `2026-09-14`, `vault-silent-5d`, `vault-silent-6d`, `vault-silent-7d`, `moc-organoid-3d-culture-uncommitted-edit-3d`, `vault-working-tree-moc-modification-2026-09-13-persists`, `thirty-first-sources-sync`, `thirty-second-sources-sync`, `thirty-third-sources-sync`, `thirty-second-git-repo-fetch`, `wiki-6-new-commits`, `deepread-40240593-twenty-two-silent-fetches`, `deepread-40240593-twenty-three-silent-fetches`; timestamp refreshed to `2026-09-16T18:18:00Z`; Source-config vault/wiki HEADs refreshed; Latest-manifest section refreshed; Carry-forward table bumped to 35/30/30/23-day; Recent-commits-wiki table refreshed (6 new commits at top); this Synthesis-policy section added; Previous-run section updated
- **`/themes/05-robin-research.md`** — frontmatter description refreshed to mention the 2026-09-16T18:18Z fetch + the vault HEAD unchanged for the 5th consecutive fetch + the 6 new wiki commits (31st/32nd/33rd sources-sync sequence) + the 35/30/30/23-day carry-forward bump + the MOC-file working-tree modification persisting uncommitted; 04-Literature/Deep-Reads/ breakdown table refreshed with the 35/30/30/23-day carry-forward bump
- **`/sources/index.md`** — refreshed the git-repo.md description entry to reflect the 2026-09-16T18:18Z fetch + the vault HEAD unchanged at `09bec367` for the 5th consecutive fetch + the wiki HEAD `ac46732` + the 35/30/30/23-day carry-forward bump + the **32nd git-repo-1 fetch** of the 2026-08-07 streak + the 11-dirty-file baseline
- **`/sources/README.md`** — refreshed Active connectors Git repo row + Connector roll Git repo row to mention the 2026-09-16T18:18Z fetch + the **thirty-third** consecutive sources-sync + the 11-dirty-file baseline + the 35/30/30/23-day carry-forward bump
- Wiki edits: see the corresponding "Latest update — git-repo-1 (2026-09-16T18:18Z)" paragraph on `/quickstart.md` for the full delta list.
## Synthesis-policy — this run (2026-09-13T18:08Z)
@@ -121,6 +139,7 @@ The 5 most recent vault commits are the new 2 (Tomas 2026 + Vijakumaran 2026) on
## Previous run
- 2026-09-13T18:08Z — vault HEAD unchanged at `09bec367` for the 2nd consecutive fetch after the Tomas 2026 + Vijakumaran 2026 resumption, 0 new vault commits + 1 working-tree modification at `MOCs/MOC-类器官与3D培养.md` (mtime 2026-09-13 11:55:42 +0800), 4 new wiki commits (`7cfb801` sources-sync 2026-09-12 — the **twenty-ninth** consecutive sources-sync + `999a37d` daily update 2026-09-12 + `0447186` daily update 2026-09-13 + `5f33bd3` sources-sync 2026-09-13 — the **thirtieth** consecutive sources-sync), 8-dirty-file baseline (down from 10-dirty at the 2026-09-11 fetch), carry-forward bump to 32/27/27/20-day. See the "Synthesis-policy — this run (2026-09-13T18:08Z)" section above + the "Latest update — git-repo-1 (2026-09-13T18:08Z)" paragraph on `/quickstart.md` for the full synthesis of that run.
- 2026-09-11T18:14Z — vault HEAD bumped `391e4713` → `09bec367` (**vault silence streak BROKEN** after 11 calendar days), 2 new vault commits (`1fd63019` Tomas 2026 HGSC + `09bec367` Vijakumaran 2026 brain-organoid ALI oxygen engineering — first v4 Flywheel auto-sink entry), 4 new wiki commits (`299eeab` sources-sync 2026-09-10 twenty-seventh + `1e6a7cb` daily update 2026-09-10 + `2bf104e` daily update 2026-09-11 + `55d930f` sources-sync 2026-09-11 twenty-eighth), 10-dirty-file baseline, 4 carry-forward untracked directories bumped to 30/25/25/18-day, 1 new untracked `NO` file. See the "Synthesis-policy — this run (2026-09-11T18:14Z)" section above + the "Latest update — git-repo-1 (2026-09-11T18:14Z)" paragraph on `/quickstart.md` for the full synthesis of that run.
- 2026-09-09T18:11Z — vault HEAD unchanged at `391e4713`, 2 new wiki commits (`f7450e9` + `7e2072c` — the **twenty-sixth** consecutive sources-sync), 10-dirty-file baseline, the 4 carry-forward untracked directories bumped to 29/24/24/17-day carry-forward. See [`/themes/05-robin-research.md`](/themes/05-robin-research.md) + `/quickstart.md` for the full synthesis of that run.
- 2026-09-10T18:19Z — manifest written by a prior ingestion cycle but no corresponding wiki update (the wiki HEAD was still `299eeab` at the 2026-09-10T18:19Z manifest timestamp, between the `7e2072c` 2026-09-09 sources-sync and the `1e6a7cb` 2026-09-10 daily update). The 2026-09-10T18:19Z manifest observed the same vault HEAD `391e4713` (vault still silent at that timestamp).