Literature Sync: Zotero + Obsidian Pipeline

Takes the .bib output of /search-lit (or any user-specified .bib file) and synchronizes the references into the Zotero library and Obsidian literature notes. When enough literature notes accumulate, extracts cross-cutting concept notes.

Communication Rules

• Communicate with the user in their preferred language (typically Korean).
• Note template headings (서지 정보, 핵심 내용, 내 생각, 관련 노트), vault folder paths (02 연구/문헌/, 02 연구/개념노트/), and Obsidian-side conventions are preserved as literal template content because they match the user's existing vault.

When to Use

• After /search-lit completes — sync the produced .bib into Zotero + Obsidian.
• Bulk-register references from an existing .bib into Zotero + Obsidian.
• Tidy the references/ folder inside a project workspace.
• On explicit concept-extraction request → extract cross-cutting concepts from existing literature notes.

Prerequisites

• Project owner only — /lit-sync is an owner-scoped operation per docs/zotero_policy.md. Collaborators consume the committed manuscript/_src/refs.bib snapshot read-only.
• Zotero desktop 7.x + Better BibTeX plugin installed.
• Better BibTeX "Keep updated" auto-export configured to <project>/manuscript/_src/refs.bib (owner setup checklist in docs/zotero_policy.md §Setup).
• Zotero MCP server available (skip the Zotero phase if not connected; auto-export refresh still fires once Zotero is reopened).
• Obsidian CLI or direct file writing to the Obsidian vault.
• Obsidian vault path: configured in user's environment (e.g., $OBSIDIAN_VAULT).

Artifact Contract

Per docs/artifact_contract.md, /lit-sync is the sole writer of:

Direct hand edits to refs.bib are drift — revert on sight.

Pipeline Overview

.bib file (or /search-lit output)
    │
    ▼ Phase 1: Parse
    Extract DOI, PMID, title, authors, journal, year
    │
    ▼ Phase 2: Zotero Sync (owner)
    Dedupe → zotero_add_by_doi → place in collection → pin citekey
    │
    ▼ Phase 2.5: refs.bib snapshot refresh
    Trigger Better BibTeX auto-export → verify manuscript/_src/refs.bib mtime updated
    │
    ▼ Phase 3: Obsidian Literature Notes
    Create 02 연구/문헌/{citekey}.md (empty note OK — fill later with highlights)
    │
    ▼ Phase 4: Concept Extraction (conditional)
    ≥10 literature notes → scan for cross-cutting concepts → propose concept notes

Phase 1: Parse BibTeX

Input

The user-specified .bib file path, or the .bib just produced by /search-lit.

Process

# Parse .bib entries with regex.
# Extract per entry:
#   - citekey (e.g., Kim_2024_Validation)
#   - doi
#   - pmid
#   - title
#   - authors (first + last minimum)
#   - journal
#   - year
#   - volume, number, pages (if present)

Log any parse failures and skip those entries.

Phase 2: Zotero Sync

Step 2.1: Determine project collection

Identify the project from the current working directory or from an explicit user override. Reuse an existing collection key if one is recorded; otherwise create a new collection.

Collection mapping: Check existing Zotero collections for the current project. If no collection exists, create one with zotero_create_collection. Record the collection key for future use.

Step 2.2: Dedupe + add

For each entry:

1. Use zotero_search_items to search by DOI or title — if already present, skip.
2. Otherwise call zotero_add_by_doi (when a DOI is available) or zotero_add_by_url (falling back to the PubMed URL when no DOI is available).
3. Use zotero_manage_collections to place the item in the project collection.

Step 2.3: Result report

Zotero Sync:
  Added:     8 papers (new)
  Skipped:   3 papers (already in library)
  Failed:    1 paper (no DOI/PMID)
  Collection: RFA-Meta (TZQEP4NH)

If the Zotero MCP is not connected, skip this entire phase and proceed to Phase 3.

Always write references/zotero_collection.json in the project workspace:

{
  "schema_version": 1,
  "status": "synced",
  "collection": "RFA-Meta",
  "collection_key": "TZQEP4NH",
  "added": 8,
  "skipped": 3,
  "failed": 1
}

If Zotero is unavailable, write the same file with status: "skipped" and a human-readable reason.

Phase 2.5: refs.bib snapshot refresh

Better BibTeX "Keep updated" auto-export normally refreshes manuscript/_src/refs.bib within seconds of a Zotero change. This phase verifies the snapshot actually updated before downstream skills consume it.

Step 2.5.1: Resolve path

Read SSOT.yaml → truth.refs_bib. Default: manuscript/_src/refs.bib. If absent (legacy project), fall back to manuscript/_src/refs.bib and emit a WARN recommending SSOT migration.

Step 2.5.1b: Precondition assertion (early-exit, do NOT poll)

Before entering the 10s polling loop in Step 2.5.2, verify both preconditions. If either fails, abort Phase 2.5 with setup instructions instead of waiting for a timeout that will never resolve.

1. BBT auto-export registered. ~/Zotero/better-bibtex/read-only.json must be a non-empty JSON list. Check with:

   python3 -c 'import json,sys,pathlib; p=pathlib.Path.home()/".zotero"/"zotero"/"Profiles"; \
     f=pathlib.Path.home()/"Zotero"/"better-bibtex"/"read-only.json"; \
     sys.exit(0 if f.exists() and json.loads(f.read_text() or "[]") else 1)'
   

   Or equivalent shell: [ -s ~/Zotero/better-bibtex/read-only.json ] && [ "$(jq 'length' ~/Zotero/better-bibtex/read-only.json)" -gt 0 ].

   On failure print:

   Phase 2.5 skipped: BBT auto-export not configured (~/Zotero/better-bibtex/read-only.json is empty or missing). Set up "Keep updated" auto-export per docs/zotero_policy.md §Setup, then re-run /lit-sync.

2. Target refs.bib exists. The resolved truth.refs_bib path from Step 2.5.1 must exist on disk (even empty is OK — BBT will overwrite). On failure print:

   Phase 2.5 skipped: target snapshot <path> not found. Configure BBT auto-export with "On Change" to the SSOT path, then re-run.

In either early-exit, set refs_bib_refreshed: false + reason: "precondition:<which>" in the Step 2.5.3 JSON and return control to the caller. /verify-refs treats refs_bib_refreshed: false as an unverified snapshot — downstream skills (/write-paper, /render) block until the precondition is resolved.

Rationale (2026-04-24 Phase 1B-b dry-run): on a machine with BBT installed but no auto-export registered, the original Step 2.5.2 polled for 10s then emitted a generic "mtime unchanged" WARN that did not point at the actual cause. Findings: ~/.local/cache/phase1b_b_dryrun/findings.md.

Step 2.5.2: Verify refresh

After Phase 2 adds items:

1. Capture stat -f "%m" manuscript/_src/refs.bib before Zotero writes.
2. Wait up to 10s (Better BibTeX debounce). Poll mtime.
3. If mtime unchanged after 10s:
   • Prompt user to check Zotero is running and BBT export is "Keep updated".
   • If BBT auto-export path is wrong, print the expected path (<project>/manuscript/_src/refs.bib) and refer to docs/zotero_policy.md §Setup.
   • As last resort, offer manual export: File → Export Library → Better BibTeX → target path.
4. Once mtime advances, grep for the newly added citekeys. All must be present; if any is missing, report as failure (do NOT fabricate entries).

Step 2.5.3: Record in zotero_collection.json

Append to the JSON written in Step 2.3:

{
  "refs_bib_path": "manuscript/_src/refs.bib",
  "refs_bib_mtime": "2026-04-24T14:32:11Z",
  "refs_bib_refreshed": true,
  "citekeys_verified": ["Kim_2024_Validation", "..."]
}

If refresh failed, set refs_bib_refreshed: false and i