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 (with privacy rules per /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:

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)
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)
391e4713 2026-08-31 — deep-read: Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids (CelVivo)
4fca0123 2026-08-31 — deep-read: Miao 2025 Cell vascularized lung/gut organoids (CelVivo ClinoReactor)
fad7e21e 2026-08-31 — deep-read: Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids (CelVivo)
030f31ed 2026-08-31 — deep-read: Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ClinoReactor)
eb24ab72 2026-08-31 — deep-read: Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids (CelVivo)

Recent commits — wiki (last 5)

5f33bd3 2026-09-13 — chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-09-13, thirtieth consecutive sources-sync)
0447186 2026-09-13 — chore: daily update 2026-09-13 (8 files modified per git show --stat 0447186)
999a37d 2026-09-12 — chore: daily update 2026-09-12 (16 files modified per git show --stat 999a37d)
7cfb801 2026-09-12 — chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-09-12, twenty-ninth consecutive sources-sync)
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 + /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).

18 KiB Raw Blame History