---
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
  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
---

# Git repo — evidence index

This page is the **compact source-evidence index** for the local git-repo connector, which ingests Robin's Obsidian vault (`/home/ldw/workspace`) and the local OpenWiki wiki (`/home/ldw/.openwiki/wiki`). Each ingestion run writes a JSON manifest under `~/.openwiki/connectors/git-repo/raw/`.

## Source config

- 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)
- 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)

## 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) |

## Robin 8-07 added — untracked regional agent files (context only)

The 8 untracked regional agent files Robin added on 2026-08-07 (per the source-specific instruction "Track vault + OpenWiki wiki mtime + commits (Robin 8-07 added)") remain in the vault working tree as uncommitted artifacts, with no mtime change observed since the 2026-08-07 baseline:

- `02-Clients/Agents/全国经销商地图-2026-0807.md`
- `02-Clients/Agents/华东-2026-0807.md`
- `02-Clients/Agents/华北-2026-0807.md`
- `02-Clients/Agents/华南-2026-0807.md`
- `02-Clients/Agents/山东-2026-0807.md`
- `02-Clients/Agents/湖北-2026-0807.md`
- `02-Clients/Agents/西北-2026-0807.md`
- `02-Clients/Agents/西南-2026-0807.md`

These files are documented in [`/sources/distributors-china-2026.md`](/sources/distributors-china-2026.md) (with privacy rules per [`/sources/agents.md`](/sources/agents.md)) — no fresh synthesis update needed at this fetch.

## Recent commits — vault (last 7)

The 5 most recent vault commits are the new 2 (Tomas 2026 + Vijakumaran 2026) on top of the 2026-08-31 THIRD consecutive single-day 5-paper CelVivo LDR burst. **Vault HEAD bumped `391e4713` → `09bec367`** — vault silence streak BROKEN after 11 calendar days:

1. `09bec367` 2026-09-11 — `literature: 精读 NocoDB Id=3029 Air-liquid interface-centered oxygen engineering in human br (飞轮 v4 自动 sink)` (brain-organoid ALI oxygen engineering — first paper routed through the **v4 Flywheel auto-sink pipeline**; new file at `Literature/Deep-Reads/Organoid/vijakumaran2026-brain-organoid-ali-oxygen-engineering.md`)
2. `1fd63019` 2026-09-10 — `feat(literature): Tomas 2026 HGSC carboplatin/PARPi spheroid+organoid deep-read` (Western University; new file at `04-Literature/Deep-Reads/tomas-2026-hgsoc-carboplatin-parpi-spheroid-organoid.md`)
3. `391e4713` 2026-08-31 — deep-read: Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids (CelVivo)
4. `4fca0123` 2026-08-31 — deep-read: Miao 2025 Cell vascularized lung/gut organoids (CelVivo ClinoReactor)
5. `fad7e21e` 2026-08-31 — deep-read: Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids (CelVivo)
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)

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)

## Synthesis-policy — this run (2026-09-13T18:08Z)

- **Vault delta: 0 new vault commits + 1 working-tree modification** — vault HEAD unchanged at `09bec367` (the 2nd consecutive vault-silent fetch after the Tomas 2026 + Vijakumaran 2026 resumption). The only vault change is the MOC-file edit: `M "04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md"` (mtime 2026-09-13 11:55:42 +0800) — Robin is actively editing the MOC index file but has not yet committed. This is the first vault working-tree modification since the 2026-08-24/25 burst (the 2026-08-31 cluster was an in-vault commit, not an uncommitted edit), and it routes through the MOC-folder rather than the `deepread_<slug>/` working-folder pipeline that the 2026-08-24/25 burst had hypothesized. The `deepread_40240593/` working folder is still silent (mtime unchanged across 19 consecutive silent fetches since the 2026-08-24 16:31 +0800 baseline).
- **Wiki delta: automated maintenance only** (CLI metadata cycle + sources-sync + daily update + sources-sync). The 4 new wiki commits in the 48-hour window are routine: 2 daily updates (`999a37d` + `0447186`) + 2 sources-syncs (`7cfb801` twenty-ninth + `5f33bd3` thirtieth). The wiki HEAD bump `55d930f` → `5f33bd3` covers 2 calendar days.
- **Dirty-file baseline change**: 10-dirty baseline (at 2026-09-11T18:14Z) → **8-dirty baseline** (at 2026-09-13T18:08Z). Different shape: `index.md` + `quickstart.md` + `sources/git-repo.md` + `themes.md` were cleared by the `999a37d` daily update; new `M sources/openwiki-version-drift.md` appeared. The 8-dirty-file list at 2026-09-13T18:08Z: `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`.
- **Synthesis-layer impact**: **none** — vault delta is empty (no new commits, no new mtime changes that alter the synthesis-layer shape) and the wiki delta is automated maintenance only. The MOC-file working-tree edit is uncommitted; 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 (2026-09-13T18:08Z)" paragraph + the description frontmatter mentions the 2026-09-13T18:08Z git-repo-1 fetch + the vault-unchanged state + the 4 new wiki commits (28th/29th/30th sources-sync sequence) + the 32/27/27/20-day carry-forward bump + the 8-dirty-file baseline + the MOC-file working-tree modification
  - **`/sources/git-repo.md`** (this page) — description frontmatter refreshed to mention the 2026-09-13T18:08Z fetch; tags refreshed to add `2026-09-13`, `2026-09-12`, `twenty-ninth-sources-sync`, `thirtieth-sources-sync`, `thirtieth-git-repo-fetch`, `thirty-first-git-repo-fetch`, `deepread-40240593-twenty-silent-fetches`, `moc-organoid-3d-culture-uncommitted-edits`, `vault-working-tree-moc-modification-2026-09-13`; timestamp refreshed to `2026-09-13T18:08:00Z`; Source-config vault/wiki HEADs refreshed; Latest-manifest section refreshed; Carry-forward table bumped to 32/27/27/20-day; Recent-commits-wiki table refreshed (4 new commits at top); this Synthesis-policy section added; Previous-run section updated
  - **`/themes/05-robin-research.md`** — frontmatter description refreshed to mention the 2026-09-13T18:08Z fetch + the vault HEAD unchanged + the 4 new wiki commits + the 32/27/27/20-day carry-forward bump + the MOC-file working-tree modification; 04-Literature/Deep-Reads/ breakdown table refreshed with the 32/27/27/20-day carry-forward bump
  - **`/sources/index.md`** — refreshed the git-repo.md description entry to reflect the 2026-09-13T18:08Z fetch + the vault HEAD unchanged + the 4 new wiki commits (28th/29th/30th sources-sync) + the 32/27/27/20-day carry-forward bump + the **31st git-repo-1 fetch** of the 2026-08-07 streak + the 8-dirty-file baseline
  - **`/sources/README.md`** — refreshed Active connectors Git repo row + Connector roll Git repo row to mention the 2026-09-13T18:08Z fetch + the **thirtieth** consecutive sources-sync + the 8-dirty-file baseline + the 32/27/27/20-day carry-forward bump
- Wiki edits: see the corresponding "Latest update — git-repo-1 (2026-09-13T18:08Z)" paragraph on `/quickstart.md` for the full delta list.

## Synthesis-policy — this run (2026-09-11T18:14Z)

- **Vault delta: 2 new vault commits** (Tomas 2026 + Vijakumaran 2026) — vault silence streak BROKEN after 11 calendar days since the 2026-08-31 THIRD consecutive 5-paper CelVivo LDR cluster. Both new papers route through the standard `04-Literature/Deep-Reads/<application-domain>/<DOI>.md` pattern. The **v4 Flywheel auto-sink pipeline** (visible in the `09bec367` commit message "飞轮 v4 自动 sink") is the first observation of Robin's LDR pipeline v4 in action — the v3 SOP was 9 steps (per the 2026-08-25 `9aa2af4c` vendor-mapping retrofit); the v4 auto-sink iterates the SOP with an automated commit/sink step.
- **Wiki delta: automated maintenance only** (CLI metadata cycle + sources-sync + daily update + sources-sync). The 4 new wiki commits are routine: 2 daily updates + 2 sources-syncs (the standard cadence).
- **Synthesis-layer impact**:
  - **Vault silence streak BROKEN** — flips the narrative from "11 calendar days of vault silence" to "vault resumed after 11-day pause" + "2 new vault commits since the 2026-08-31 cluster" + "v4 Flywheel auto-sink pipeline first observation"
  - **`/sources/literature.md`** gets a new `2026-09-11 (Vijakumaran 2026 brain-organoid ALI oxygen engineering — first v4 Flywheel auto-sink entry)` row; the Tomas 2026 entry was added in a prior run (2026-09-10 row already present)
  - **`/themes.md`** `class-organoid-3d-bioprinting` row gets Last-seen refresh `2026-08-25` → `2026-09-11` + Evidence count bump `37+` → `39+` (Tomas 2026 + Vijakumaran 2026 = 2 new entries)
  - **`/themes/05-robin-research.md`** vault-snapshot metadata refreshed + 04-Literature/Deep-Reads/ breakdown table updated with Vijakumaran 2026 row + the 4 carry-forward untracked directories bumped to 30/25/25/18-day carry-forward
  - **`/quickstart.md`** gets a new "Latest update — git-repo-1 (2026-09-11T18:14Z)" paragraph + the description frontmatter mentions the 2026-09-11T18:14Z git-repo-1 fetch + the vault silence streak broken + the 2 new vault commits + the 4 new wiki commits + the 30/25/25/18-day carry-forward bump
  - **`/sources/index.md`** + **`/sources/README.md`** get their git-repo.md description entries refreshed
- Wiki edits: see the corresponding "Latest update — git-repo-1 (2026-09-11T18:14Z)" paragraph on `/quickstart.md` for the full delta list.

## Previous 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).
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).
ces-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).
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).
6-09-09 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).