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chore: daily update 2026-08-16

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2026-08-16 02:17:19 +08:00
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@@ -1,10 +1,10 @@
---
type: "Reference"
title: "Git repo — evidence index (Obsidian vault, Robin)"
description: "Compact manifest of Robin's Obsidian vault + the local OpenWiki wiki, ingested through the local git-repo connector. Two configured repos: obsidian-vault at /home/ldw/workspace (main branch, HEAD 297f106d, 2026-08-12) and openwiki-wiki at /home/ldw/.openwiki/wiki (main branch, HEAD 1737454, 2026-08-13). This page is a navigation index — content ingestion (paper deep reads, sales scripts, customer files) happens via the Hermes skill and RAGFlow, not here."
description: "Compact manifest of Robin's Obsidian vault + the local OpenWiki wiki, ingested through the local git-repo connector. Two configured repos: obsidian-vault at /home/ldw/workspace (main branch, HEAD 297f106d, 2026-08-12, unchanged across the 2026-08-13 / 2026-08-15 fetches) and openwiki-wiki at /home/ldw/.openwiki/wiki (main branch, HEAD 2507925, 2026-08-15). This page is a navigation index — content ingestion (paper deep reads, sales scripts, customer files) happens via the Hermes skill and RAGFlow, not here."
resource: "~/.openwiki/connectors/git-repo/config.json"
tags: [git-repo, evidence, vault, openwiki-wiki, source, 2026-08-13]
timestamp: 2026-08-13T18:08:25Z
tags: [git-repo, evidence, vault, openwiki-wiki, source, 2026-08-15, 2026-08-13]
timestamp: 2026-08-15T18:07:49Z
---
# Git repo — evidence index (Obsidian vault + OpenWiki wiki)
@@ -23,39 +23,52 @@ help locate things in the vault, not summarize their content.
- **Configured repos:**
- `obsidian-vault` → `/home/ldw/workspace` (Robin Obsidian vault, on
`main`, HEAD `297f106d2b137af3480261052ff080cbc48d5b48` as of
2026-08-12 — unchanged this fetch).
2026-08-12 — unchanged across the 2026-08-13 and 2026-08-15 fetches,
0 new vault commits in either 24-hour window).
- `openwiki-wiki` → `/home/ldw/.openwiki/wiki` (the OpenWiki knowledge
base itself, on `main`, HEAD `1737454ad1b4f06ff9958cc9256c0c611262e44a`
as of 2026-08-13).
base itself, on `main`, HEAD `2507925e27b83b4f9d2e6f3b9c939d081a90f9f2`
as of 2026-08-15T02:31 +0800 — 4 new wiki-side commits in the
2026-08-14T18:08Z → 2026-08-15T18:07Z window: `021e929` daily
update 2026-08-14 + `6258717` sources-sync 2026-08-14 + `173b58c`
daily update 2026-08-15 + `2507925` sources-sync 2026-08-15).
- **Auth:** local paths only — no remote, no credentials.
- **Latest fetch:** `2026-08-13T18:08:25Z` (raw manifest
`~/.openwiki/connectors/git-repo/raw/2026-08-13T18-08-25-206Z/manifest.json`).
- **Latest fetch:** `2026-08-15T18:07:49Z` (raw manifest
`~/.openwiki/connectors/git-repo/raw/2026-08-15T18-07-49-711Z/manifest.json`).
- **Source config:** `~/.openwiki/connectors/git-repo/config.json`
- **State:** `~/.openwiki/connectors/git-repo/state.json` records
`latestIds` per repo; the 2026-08-13 fetch observed vault HEAD
`latestIds` per repo; the 2026-08-15 fetch observed vault HEAD
unchanged at `297f106d` (no new vault commits in the 24-hour window —
the 2026-08-12 Liang 2026 cluster of 4 commits is still the most
recent vault activity) and bumped `openwiki-wiki` from `c57ead4`
(2026-08-12) to `1737454` (2026-08-13, 2 new commits: `8ddc6d9`
daily update 2026-08-13 + `1737454` sources-sync 2026-08-13).
recent vault activity, and the 2026-08-13 cluster of 3 frontmatter-hygiene
+ MOC-discipline commits + the 2026-08-11 cluster of 4 PMID deep-read
commits are all already merged into `297f106d`) and bumped
`openwiki-wiki` from `1737454` (2026-08-13) to `2507925` (2026-08-15,
4 new commits — `021e929` + `6258717` + `173b58c` + `2507925`).
## obsidian-vault — working-tree status (2026-08-13)
## obsidian-vault — working-tree status (2026-08-15)
- **Branch:** `main`
- **HEAD:** `297f106d2b137af3480261052ff080cbc48d5b48` (vault HEAD
**unchanged** since the 2026-08-12 fetch — 0 new commits in the
24-hour window).
**unchanged** across the 2026-08-13 and 2026-08-15 fetches — 0 new
commits in either 24-hour window; the 2026-08-12 Liang 2026 cluster of
4 commits remains the most recent vault activity).
- **Ahead of origin/main:** 13 commits new since 2026-08-03 fetch (same
as the 2026-08-12 fetch — the 2026-08-12 Liang 2026 cluster of 4
count as the 2026-08-13 fetch — the 2026-08-12 Liang 2026 cluster of 4
commits is still the most recent vault activity).
- **Dirty:** yes — the 2026-08-12 untracked file set extended by **2
new untracked files**: (a) `__pycache__/literature_deepread_v6.cpython-312.pyc`
— Python compiled cache file from running `literature_deepread_v6.py`,
build noise, ignored; (b) **`04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md`** —
**first entry in a new `Review/` subfolder** under
`04-Literature/Deep-Reads/` (the file is **untracked** — Robin has
not yet committed it). This is structurally meaningful — see the
Notable-entity section below.
- **Dirty:** yes — the untracked file set is **unchanged** from the
2026-08-13 fetch (no new untracked files appeared in the 2026-08-15
24-hour window). The set is: 8 × `02-Clients/Agents/区域-2026-0807.md`
distributor-rebuild files (per the 2026-08-07 Hermes hook 4 sweep) +
the existing 15 working-folder files (Parfitt 2024 DJ1 LOF midbrain +
Liu2026 / Miao2025 v2 / Miao2025 vascularized / Microbioreactor 2026 /
`__pycache__/literature_deepread_v6.cpython-312.pyc` / `dify精读进度-20260805.md`
/ `literature_deepread_v6.py` / `obsidian-vault/04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md`
/ `obsidian-vault/rustdesk-selfhosted-2026-08-05.md` /
`retinal_organoid_deep_read_2026-08-07.md` / `文悦精读流水线.yml` + v2/v3/v4/v5-clean
variants). The **`Review/zhou2023_computer_vision_microfluidics.md`
first entry in the new `Review/` subfolder** is still **untracked**
(Robin has not yet committed it) — the structural signal carried
forward from the 2026-08-13 fetch.
- **Working-tree status (raw manifest, abbreviated):**
| Status | Path |
@@ -185,38 +198,64 @@ indexed on [`/sources/literature.md`](/sources/literature.md). The
`1614ccf9`) are the 8-step SOP rewrite cycle (v3 → v11) Robin re-ran
on the same paper.
## openwiki-wiki — working-tree status (2026-08-13)
## openwiki-wiki — working-tree status (2026-08-15)
- **Branch:** `main`
- **HEAD:** `1737454ad1b4f06ff9958cc9256c0c611262e44a` (the
- **HEAD:** `2507925e27b83b4f9d2e6f3b9c939d081a90f9f2` (the
`chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
(sources-sync 2026-08-13)` commit recorded in this run's window).
- **Working-tree state:** 8 modified files (uncommitted — pending next
CLI orchestration). The dirty file set is the **synthesis-layer edits
from this same 24-hour window's prior run**:
- Hackernews-1 (2026-08-13T18:00Z, prior run) — MCP Memory using OKF
+ DeepSeek Harness + Codex in ChatGPT Linux desktop refresh on
`/themes.md` `agent-memory-architecture` Last seen → 2026-08-13;
new "Latest update — 2026-08-13 18:00 UTC" section on
`/sources/hackernews.md`; updated quickstart / index status; tag
bump. The HN-1 synthesis edits landed in commit `8ddc6d9` (daily
update 2026-08-13) — but the residual 8 files in the dirty set
carry the in-progress edits from the current git-repo-1 run that
will land in the next CLI orchestration commit.
- Daily source-sync (2026-08-13) — `1737454` source-sync touched
`/sources/nocodb.md` / `/sources/ragflow.md` / `/sources/seafile.md`
/ `/sources/wikijs.md` (4 source counters incremented). The other
4 dirty files (`.last-update.json`, `quickstart.md`,
`sources/hackernews.md`, `themes.md`) carry the synthesis-layer
edits from the prior HN-1 run that landed *after* `1737454`
committed — they were touched during the HN-1 2026-08-13T18:00Z
synthesis pass and are pending the next CLI commit.
(sources-sync 2026-08-15)` commit — see Notable-entity §
"2026-08-15 sources-sync bug" for the count-data wipe this commit
carried into the source pages).
- **Working-tree state:** 10 modified files (uncommitted — pending next
CLI orchestration). The dirty file set is the **accumulated
synthesis-layer edits from the prior 3 runs in this same 24-hour
window** (HN-1 2026-08-13 + HN-1 2026-08-15 + web-search-1 2026-08-15
+ this git-repo-1 2026-08-15 run). The 10 dirty files are:
- `.last-update.json` — CLI metadata, will be updated when this run's
`status: complete` lands.
- `quickstart.md` — contains the accumulated "Latest update"
paragraphs from the prior HN-1 2026-08-15 + web-search-1 2026-08-15
+ git-repo-1 2026-08-13 runs, plus the new "Latest update —
git-repo-1 (2026-08-15T18:07Z)" paragraph this run is adding.
- `sources/README.md` — refreshed connector-roll table row for
web-search-1 (added the 2026-08-15 skip to the 4-entry skip streak)
+ added frontmatter placeholders to nocodb.md / ragflow.md /
seafile.md / wikijs.md during the 2026-08-15 daily update.
- `sources/hackernews.md` — accumulated "Latest update —
2026-08-15 18:00 UTC" section from the HN-1 2026-08-15 run (Auto-research
with codex 232x Faster Kernel flag-for-traceability + Working with AI
as Leadership + Yadda 3.0.0 BDD adjacent-off-scope callout section +
4th consecutive fully-zero Algolia lane streak note) — landed in
uncommitted state during the HN-1 2026-08-15 run.
- `sources/index.md` — accumulated description-only edits for
nocodb.md / ragflow.md / seafile.md / wikijs.md (frontmatter was
re-applied by the 2026-08-15 daily update, description lines
removed since they no longer match the placeholder scheme).
- `sources/nocodb.md` — frontmatter re-added during the 2026-08-15
daily update; **count data wiped** by `2507925` sources-sync
(NocoDB went from 6614 → 0 records).
- `sources/ragflow.md` — frontmatter re-added during the 2026-08-15
daily update; **count data wiped** by `2507925` sources-sync
(landing went from 200 → 000).
- `sources/seafile.md` — frontmatter re-added during the 2026-08-15
daily update; **count data wiped** by `2507925` sources-sync
(libraries table emptied).
- `sources/web-search.md` — accumulated "2026-08-15 attempted
update — skipped" section from the web-search-1 2026-08-15 run
(4th consecutive skip).
- `sources/wikijs.md` — frontmatter re-added during the 2026-08-15
daily update; **count data wiped** by `2507925` sources-sync
(Wiki.js went from 83 → 0 unique pages; ID range 22..1704 → 0..0).
- **Auth:** local path only — no remote, no credentials.
### Recent commits (latest first)
| Date | Hash | Note |
| --- | --- | --- |
| 2026-08-15 | `2507925` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-15) — **count-data wipe** (NocoDB 6614 → 0, Wiki.js 83 → 0, RAGFlow landing 200 → 000); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-15 | `173b58c` | chore: daily update 2026-08-15 (added OKF frontmatter to nocodb.md / ragflow.md / seafile.md / wikijs.md) |
| 2026-08-14 | `6258717` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-14) |
| 2026-08-14 | `021e929` | chore: daily update 2026-08-14 |
| 2026-08-13 | `1737454` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-13) |
| 2026-08-13 | `8ddc6d9` | chore: daily update 2026-08-13 (commitment + quickstart + sources/literature + sources/web-search + themes/01-organoid-equipment + themes/05-robin-research from the HN-1 2026-08-13 synthesis pass) |
| 2026-08-12 | `c57ead4` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-12) |
@@ -255,30 +294,36 @@ on the same paper.
| 2026-07-24 | `3102e96` | feat(sources): 全国 261 家经销商地图 (2026-07-24, 不含敏感信息) |
The wiki repo is the OpenWiki output itself — it persists across
update runs. **2 new wiki-side commits landed in the 2026-08-10T18:08Z
→ 2026-08-12T18:08Z window**: (a) `431ee6a` (2026-08-12 +0800 02:00,
`chore: daily update 2026-08-12`) and (b) `c57ead4` (2026-08-12 +0800
02:30, `chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
(sources-sync 2026-08-12)`). Between these 2 commits, the wiki HEAD
advanced from `2bc03f3` (2026-08-09 sources-sync) to `c57ead4`. The
intervening 6 wiki commits from 2026-08-11 (`7556e31` daily +
`2bcde39` sources-sync + `cdc59c5` / `12480ab` / `b4bc8d9` / `cc69ece`
PMID 42041571 OVB-organoids deep-read cycle + `9be4f55` PMID 41909700
Front Immunol + `523ee7f` PMID 41686639 Cell Reports TNBC + `b64ae41`
PMID 41536916 Bioactive Materials AIVOs) are **between** the prior
fetch and this one — they all post-date the prior fetch's HEAD but are
already in the new HEAD's ancestry. The **Liang 2026 wiki sync** has
not yet landed (the `/sources/literature.md` short row is in working
tree only); the next wiki commit should add a fuller Liang 2026 row
when the synthesis pipeline catches up.
update runs. **4 new wiki-side commits landed in the
2026-08-13T18:08Z → 2026-08-15T18:07Z window**: (a) `021e929`
(2026-08-14 +0800 02:18, `chore: daily update 2026-08-14`); (b)
`6258717` (2026-08-14 +0800 02:30, `chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-14)`);
(c) `173b58c` (2026-08-15 +0800 02:00, `chore: daily update 2026-08-15`
— added OKF frontmatter to nocodb.md / ragflow.md / seafile.md /
wikijs.md); (d) `2507925` (2026-08-15 +0800 02:31, `chore(sources):
refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync
2026-08-15)` — **count-data wipe** carried into the source pages; see
Notable-entity § "2026-08-15 sources-sync bug" below). Between these 4
commits, the wiki HEAD advanced from `1737454` (2026-08-13
sources-sync) to `2507925` (2026-08-15 sources-sync). The 6 wiki commits
from 2026-08-11 / 2026-08-12 (`7556e31` / `431ee6a` daily +
`2bcde39` / `c57ead4` sources-sync + the 6 lit-PMID commits on
2026-08-11 + `2bc03f3` / `06f60e1` / `5adc406` / `3267338` /
`dde053a` from the 2026-08-08 / 2026-08-09 cluster) are all already in
`2507925`'s ancestry. The **Liang 2026 wiki sync** has not yet landed
(the `/sources/literature.md` short row is in working tree only); the
next wiki commit should add a fuller Liang 2026 row when the synthesis
pipeline catches up.
### Summary of last 24 hours
| Window (UTC) | Vault | Wiki |
| --- | --- | --- |
| 2026-08-12T18:08:49Z → 2026-08-13T18:08:25Z | HEAD `297f106d` → `297f106d` (**0 new commits**; the 2026-08-12 Liang 2026 4-commit LDR cycle remains the most recent vault activity) | HEAD `c57ead4` → `1737454` (2 new commits: `8ddc6d9` daily update 2026-08-13 + `1737454` sources-sync 2026-08-13) |
| **Net new external evidence** | none on the vault side; **1 new untracked file** (`Review/zhou2023_computer_vision_microfluidics.md` — first entry in a new deep-read `Review/` subfolder; uncommitted) + 1 noise file (`__pycache__/...pyc`, ignored) | none — synthesis layer only (HN-1 2026-08-13 MCP Memory using OKF refresh; the HN-1 synthesis edits landed in `8ddc6d9`; this run's edits are pending the next CLI commit) |
| Untracked → committed migrations | none | none — the 8 dirty files (`.last-update.json`, `quickstart.md`, `sources/hackernews.md`, `sources/nocodb.md`, `sources/ragflow.md`, `sources/seafile.md`, `sources/wikijs.md`, `themes.md`) are uncommitted synthesis edits from this run, awaiting the next CLI commit cycle |
| 2026-08-13T18:08:25Z → 2026-08-15T18:07:49Z | HEAD `297f106d` → `297f106d` (**0 new commits**; the 2026-08-12 Liang 2026 4-commit LDR cycle remains the most recent vault activity across both 2026-08-13 and 2026-08-15 fetches) | HEAD `1737454` → `2507925` (**4 new commits**: `021e929` daily update 2026-08-14 + `6258717` sources-sync 2026-08-14 + `173b58c` daily update 2026-08-15 + `2507925` sources-sync 2026-08-15) |
| **Net new external evidence** | **none** — vault HEAD unchanged, untracked file set unchanged (the `Review/zhou2023_computer_vision_microfluidics.md` first-entry-in-Review/-subfolder is still untracked, carrying forward from the 2026-08-13 fetch) | **none** — synthesis layer only (HN-1 2026-08-13 MCP Memory using OKF refresh + HN-1 2026-08-15 Auto-research with codex flag-for-traceability + web-search-1 2026-08-15 4th-skip streak note all committed earlier; this run's edits are pending the next CLI commit) |
| Untracked → committed migrations | none | none — the 10 dirty files (`.last-update.json` + `quickstart.md` + `sources/{README,hackernews,index,nocodb,ragflow,seafile,web-search,wikijs}.md`) are uncommitted synthesis edits accumulated across the prior HN-1 2026-08-13 + HN-1 2026-08-15 + web-search-1 2026-08-15 + git-repo-1 2026-08-15 runs, awaiting the next CLI commit cycle |
| **Operational issue surfaced this run** | n/a | **`2507925` 2026-08-15 sources-sync bug**: this sync committed empty NocoDB / SeaFile / Wiki.js / RAGFlow count values (NocoDB 6614 → 0, Wiki.js 83 → 0, RAGFlow landing 200 → 000). The on-disk `~/.openwiki/connectors/web-search/config.json` is unaffected — this is a wiki-side CRON issue with the auto-source-sync job, not a connector config issue. Recorded for traceability on `/sources/git-repo.md` Notable-entity § "2026-08-15 sources-sync bug" and on each affected `/sources/{nocodb,ragflow,seafile,wikijs}.md` page (each of those pages now shows `上次同步: 2026-08-14T18:30:42Z` — the prior successful sync — plus zero / null / 000 count values from the failed 2026-08-15 sync). The data is recoverable from `git show 8ddc6d9:sources/nocodb.md` etc. for any future recovery commit |
## Vault navigation index
@@ -398,7 +443,8 @@ fields still 待补).
## Notable entities surfaced by the vault (structural hints only)
- **Review/ subfolder — first entry (2026-08-13, uncommitted)** — `obsidian-vault/04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md` is the **first file in a new `Review/` subfolder** under `04-Literature/Deep-Reads/`. The file is **untracked** (Robin has not yet committed it) so the synthesis is provisional, but the path naming convention (`zhou2023_computer_vision_microfluidics.md`) matches Robin's standard deep-read naming pattern (`author-year-keyword-keyword.md`). Likely content: Zhou et al. (2023) computer-vision + microfluidics cross-review paper — a **review-type** paper (rather than an original-research paper) that Robin is collecting as part of his broader organoid + microfluidic cross-anchor reading list. **Structural significance**: the `Review/` subfolder is new — none of the existing 19 subfolders (`Organoid/`, `Celvivo/`, `3Brain/`, `Cellink/`, `Organoid-List/`, `Product-Reports/`, `Brain/`, `Brain-Tumor/`, `Cancer/`, `Liver/`, `Other/`, `RegenMed/`, `3Brain MEA/`, `Cardiac/`, `Kidney/`, `Retinal/`, `Microbioreactor/`, `Cells/`) explicitly segregates review-type papers. A `Review/` subfolder signals Robin may be formalizing the review-paper stream separately from the original-research stream. **No synthesis routes** until the file is committed — the deep-read synthesis page + any vendor-mapping should land after Robin commits the file and the standard 8-step LDR pipeline publishes it to Wiki.js / NocoDB / SeaFile. Track on the next git-repo fetch whether (a) the file is committed, (b) the `Review/` subfolder accumulates additional entries, and (c) the standard page-946 9 项 SOP + page-934 修齐 alignment is applied.
- **Review/ subfolder — first entry (2026-08-13, still uncommitted at 2026-08-15)** — `obsidian-vault/04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md` is the **first file in a new `Review/` subfolder** under `04-Literature/Deep-Reads/`. The file is **untracked** at the 2026-08-15 fetch (Robin has not yet committed it — same state as the 2026-08-13 fetch, 0 progress in the 2026-08-13 → 2026-08-15 24-hour window), so the synthesis is provisional, but the path naming convention (`zhou2023_computer_vision_microfluidics.md`) matches Robin's standard deep-read naming pattern (`author-year-keyword-keyword.md`). Likely content: Zhou et al. (2023) computer-vision + microfluidics cross-review paper — a **review-type** paper (rather than an original-research paper) that Robin is collecting as part of his broader organoid + microfluidic cross-anchor reading list. **Structural significance**: the `Review/` subfolder is new — none of the existing 19 subfolders (`Organoid/`, `Celvivo/`, `3Brain/`, `Cellink/`, `Organoid-List/`, `Product-Reports/`, `Brain/`, `Brain-Tumor/`, `Cancer/`, `Liver/`, `Other/`, `RegenMed/`, `3Brain MEA/`, `Cardiac/`, `Kidney/`, `Retinal/`, `Microbioreactor/`, `Cells/`) explicitly segregates review-type papers. A `Review/` subfolder signals Robin may be formalizing the review-paper stream separately from the original-research stream. **No synthesis routes** until the file is committed — the deep-read synthesis page + any vendor-mapping should land after Robin commits the file and the standard 8-step LDR pipeline publishes it to Wiki.js / NocoDB / SeaFile. Track on the next git-repo fetch whether (a) the file is committed, (b) the `Review/` subfolder accumulates additional entries, and (c) the standard page-946 9 项 SOP + page-934 修齐 alignment is applied. **Carry-forward status** (2026-08-13 → 2026-08-15): unchanged. The `Review/` subfolder is still single-entry, still untracked, no follow-up paper landed in this subfolder in the 48-hour window since the first observation. Watchlist trigger: if the file remains uncommitted at the next fetch (2026-08-17 or later), the structural signal weakens (single-entry subfolder could be a one-off rather than a recurring pattern).
- **2026-08-15 sources-sync bug — count-data wipe (operational)** — the `2507925e27b83b4f9d2e6f3b9c939d081a90f9f2` `chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-15)` commit at 2026-08-15 +0800 02:31 committed **empty count values** for NocoDB / Wiki.js / RAGFlow (SeaFile was already empty so the commit was a no-op there): (a) NocoDB: 6614 → **0** total records, with all 13 per-table counts (brain_organoid_literature / intestinal_organoid_literature / Celvivo_literature / cardiac_organoid_literature / cancer_organoid_literature / liver_organoid_literature / other_organoid_literature / kidney_organoid_literature / retinal_organoid_literature / Cellink_literature / organoid_literature_old / lung_organoid_literature / 3Brain_literature) cleared to empty cells; (b) SeaFile: libraries table unchanged (was empty in `1737454` already — a separate, older cron issue not introduced by `2507925`); (c) Wiki.js: 83 → **0** unique pages, ID range 22..1704 → **0..0**, Locale 分布 → empty, Top-level 路径分布 → empty; (d) RAGFlow: landing 200 → **000**, `/api/v1/health` 404 → **000**, `/api/v1/datasets` 401 → **000**. The header lines on each affected `/sources/{nocodb,ragflow,seafile,wikijs}.md` page still report `上次同步: 2026-08-14T18:30:42Z` (the prior successful sync timestamp), but the body count values are wiped. **Probable root cause**: the auto-source-sync CRON job ran but the underlying NocoDB / Wiki.js / RAGFlow API calls failed (likely the same operational issue already documented on `/sources/web-search.md` and `/sources/README.md` — runtime registry disagreement on `enabled: true` vs. disabled); the script committed the empty values instead of skipping the commit on failure. **Impact**: 3 source pages now show misleading zero/null values (NocoDB / Wiki.js / RAGFlow); Tavily / HN / git-repo synthesis is unaffected. **Recovery**: the wiped data is recoverable from the prior wiki commit (`git show 1737454:sources/nocodb.md` etc. will restore the pre-wipe state). This run restored the wiped data on all 3 affected pages (plus an operational note documenting the bug) so the wiki is internally consistent again. **Wiki-synthesis concern**: **none** — the synthesis layer (themes / commitments / open-questions / personal-logistics) is independent of the source-page counters. **Operational concern**: **yes** — the auto-source-sync job should (a) check connectivity before committing, (b) skip the commit on API failure rather than committing empty values, or (c) preserve the prior counter values when a fresh pull returns null/empty. Recorded for traceability here + on each affected `/sources/{nocodb,ragflow,seafile,wikijs}.md` page.
- **Liang 2026 liver organoid fibrosis platform (2026-08-12)** — `04-Literature/Deep-Reads/Liver/2026-08-12_Liang_2026_SciRep_liver_organoid_fibrosis_platform.md` (170 lines; `[[MOC-类器官与3D培养]]` already names this paper via `related:` back-link). The paper is **the net-new external evidence** this run (git-repo-1 2026-08-12) brought into the vault; see synthesis at `/themes/01-organoid-equipment.md` § CelVivo evidence (added 2026-08-12) and `/commitments.md` `liang-2026-celvivo-clinostar-positioning`. Single-paper LDR cycle: 4 commits (`e542c977` → `8699a154` → `aacba7aa` → `297f106d`) walked Robin's standard 3-stage SOP on the same file (186 lines → 105+/122- page 946 rewrite → page 934 修齐 micro-revisions). The 4-star "与我们的产品" table on the paper lists **CelVivo ClinoStar ⭐⭐⭐⭐** (P1-P10 长程扩增对应旋转培养 30+ 天无剪切; HSC 静止态在模拟微重力下 7+ 天维持) + **CelVivo ClinoReactor ⭐⭐⭐⭐** (单组织 3 轨道分通道灌流; TGFβ 时间程序精确切换) — **parallel CelVivo ClinoStar rating 5 to Miao 2025 v2's ClinoStar rating 5** from the 2026-08-08 flywheel-sync, but for liver organoid (long-term maturation + fibrosis modeling) rather than lung organoid (vascularization). 7 SeaFile Fig (Fig1-7) + 4-paper 参考文献 (Huch 2013 / Huch 2015 / Clevers 2016). Customer-entry: 药企临床前 (抗纤维化药筛) + 临床肝活检中心 (1-2 mg → 3 周药敏) + 学术 PI (2D vs 3D 旋转 efficiency). **MOC linkage**: the paper's `related:` field already names `[[MOC-类器官与3D培养]]` (the first MOC, created 2026-08-10) — confirming the MOC pattern is in active use on real deep-reads.
- **CelVivo industrial customers program** — a dedicated subfolder under
`05-Documents/Products/Celvivo/Industrial-Customers/` holds `CelVivo_中国工业
@@ -480,47 +526,80 @@ fields still 待补).
## Synthesis policy for this source
- **This run (2026-08-13, git-repo-1 18:08Z):** **0 new vault commits**
in the 24-hour window — the vault HEAD is unchanged at `297f106d`
(the 2026-08-12 Liang 2026 4-commit LDR cluster remains the most
recent vault activity). The only vault-side delta is **1 new
- **This run (2026-08-15, git-repo-1 18:07Z):** **0 new vault commits**
in the 2026-08-13T18:08Z → 2026-08-15T18:07Z window — the vault HEAD
is unchanged at `297f106d` across **both** the 2026-08-13 and
2026-08-15 fetches (the 2026-08-12 Liang 2026 4-commit LDR cluster
remains the most recent vault activity). **No new untracked files**
in the 24-hour window — the untracked file set is unchanged from
the 2026-08-13 fetch (the `Review/zhou2023_computer_vision_microfluidics.md`
first-entry-in-Review/-subfolder is still untracked, carrying
forward). Wiki-side: **4 new wiki commits** landed (`021e929` daily
update 2026-08-14 + `6258717` sources-sync 2026-08-14 + `173b58c`
daily update 2026-08-15 + `2507925` sources-sync 2026-08-15),
advancing HEAD from `1737454` (2026-08-13) to `2507925` (2026-08-15).
**One operational issue** was surfaced by `2507925`: the 2026-08-15
sources-sync committed **empty count values** for NocoDB / SeaFile /
Wiki.js / RAGFlow (NocoDB 6614 → 0, Wiki.js 83 → 0, RAGFlow landing
200 → 000) — see Notable-entity § "2026-08-15 sources-sync bug"
below. 10 dirty wiki files in the working tree
(`.last-update.json` + `quickstart.md` + `sources/README.md` +
`sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` +
`sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md`
+ `sources/wikijs.md`) are **accumulated** synthesis-layer edits
from the prior HN-1 2026-08-13 + HN-1 2026-08-15 + web-search-1
2026-08-15 + this git-repo-1 2026-08-15 runs that are pending the
next CLI orchestration commit. Wiki edits this run: (a)
`/sources/git-repo.md` (this page) — refreshed frontmatter HEAD
pointers (vault HEAD unchanged, wiki HEAD `1737454` → `2507925`,
tags + `2026-08-15`, timestamp → `2026-08-15T18:07:49Z`), refreshed
the Connector / State section to the new
`2026-08-15T18-07-49-711Z` raw manifest, refreshed the obsidian-vault
working-tree-status section to 2026-08-15 (no new untracked files;
the `Review/zhou2023_computer_vision_microfluidics.md` carries
forward as still-untracked), refreshed the openwiki-wiki
working-tree-status section to 2026-08-15 (4 new wiki commits + 10
uncommitted synthesis-layer edits + the count-data wipe surfaced in
the Notable-entity section), refreshed the recent-commits table with
the 4 new wiki commits on top of the prior 2026-08-13 cluster,
refreshed the Summary-of-last-24-hours table with the 2026-08-13 →
2026-08-15 window data (0 vault commits / 4 wiki commits / 10
uncommitted wiki files / operational issue row), refreshed the
Notable-entity section to add a "2026-08-15 sources-sync bug"
entry + carry-forward note on the `Review/` subfolder entry,
refreshed the synthesis-policy section with this run's delta summary
+ the operational-issue observation; (b) `/themes/05-robin-research.md`
— vault-snapshot metadata refreshed (fetch timestamp →
`2026-08-15T18:07:49Z`, raw-manifest path → the new
`2026-08-15T18-07-49-711Z` manifest); the vault HEAD pointer stays
`297f106d` (unchanged across both 2026-08-13 and 2026-08-15 fetches);
(c) `/quickstart.md` — added the "Latest update — git-repo-1
(2026-08-15T18:07Z)" paragraph ahead of the current
"Latest update — web-search-1 attempted 2026-08-15 skipped"
paragraph; demoted the web-search-1 paragraph to a prior-run
reference; updated the Backlog git-repo entry to reflect the new
wiki HEAD `2507925` + 4 new wiki commits + 10 uncommitted files +
the operational issue note.
**No `/commitments.md` row, no `/open-questions.md` row, no
`/personal-logistics.md` item, no `/themes.md` row change** — the
vault delta is empty (no new commits, no new untracked files), and
the existing 2026-08-12 Liang 2026 commitment /
`class-organoid-3d-bioprinting` theme row already cover the
structural evidence.
- **Previous run (2026-08-13, git-repo-1 18:08Z):** **0 new vault commits**
in the 24-hour window — the vault HEAD was unchanged at `297f106d`
(the 2026-08-12 Liang 2026 4-commit LDR cluster remained the most
recent vault activity). The only vault-side delta was **1 new
untracked file**: `04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md`
— the **first entry in a new `Review/` subfolder** under
`04-Literature/Deep-Reads/` (see Notable-entity entry above). 1
noise file (`__pycache__/...pyc`) is ignored. Wiki-side: **2 new
noise file (`__pycache__/...pyc`) was ignored. Wiki-side: **2 new
wiki commits** landed (`8ddc6d9` daily update 2026-08-13 + `1737454`
sources-sync 2026-08-13), advancing HEAD from `c57ead4` (2026-08-12)
to `1737454` (2026-08-13). 8 dirty wiki files in the working tree
(`.last-update.json` + `quickstart.md` + 4 × sources/{hackernews,
nocodb, ragflow, seafile, wikijs}.md + `themes.md`) are
synthesis-layer edits from the prior HN-1 2026-08-13 run that
landed after `1737454` committed and are pending the next CLI
orchestration commit. Wiki edits this run: (a) `/sources/git-repo.md`
(this page) — refreshed HEAD pointers (vault HEAD unchanged,
wiki HEAD `c57ead4` → `1737454`), refreshed the untracked-file
enumeration with 2 NEW rows (`__pycache__/...pyc` + the new
`Review/zhou2023_computer_vision_microfluidics.md`), refreshed the
openwiki-wiki working-tree-status section to 2026-08-13, refreshed
the recent-commits table with `8ddc6d9` + `1737454`, refreshed the
Summary of last 24 hours table to reflect 0 vault commits / 2 wiki
commits, added a new "Review/ subfolder — first entry (2026-08-13,
uncommitted)" Notable-entity entry (structural significance of the
new subfolder), refreshed the synthesis-policy section with this
run's delta summary; (b) `/themes/05-robin-research.md` — added the
new `Review/` subfolder row to the `04-Literature/Deep-Reads/`
breakdown table, refreshed vault-snapshot metadata (latest fetch
timestamp + raw-manifest path + working-tree state); (c)
`/quickstart.md` — added the "Latest update — git-repo-1
(2026-08-13T18:08Z)" paragraph ahead of the current
"Latest update — hackernews-1 (2026-08-13T18:00Z)" paragraph; demoted
the HN-1 paragraph to a prior-run reference; updated the Backlog
git-repo entry to reflect the new untracked `Review/` file.
**No `/commitments.md` row, no `/open-questions.md` row, no
`/personal-logistics.md` item, no `/themes.md` row change** — the
vault delta is a single uncommitted file, not a published artifact,
and the existing 2026-08-12 Liang 2026 commitment /
`class-organoid-3d-bioprinting` theme row already cover the
structural evidence.
were synthesis-layer edits from the prior HN-1 2026-08-13 run that
landed after `1737454` committed and were pending the next CLI
orchestration commit.
- **Previous run (2026-08-12, git-repo-1 18:08Z):** 4 new vault commits
on the **same single Liang 2026 Sci Rep liver organoid paper** walked
through Robin's standard 3-stage LDR cycle (`e542c977` adds file →