backup materials and knowledge-base docs

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+---
+name: zotero-notes
+description: Batch read papers from Zotero and create/update detailed reading notes, preferably inside the bound Obsidian project knowledge base
+args:
+  - name: collection
+    description: Zotero collection name or keyword
+    required: true
+  - name: format
+    description: Note format (summary/detailed/comparison)
+    required: false
+    default: detailed
+tags: [Research, Zotero, Obsidian, Reading Notes, Paper Analysis]
+---
+
+# /zotero-notes - Zotero to Obsidian Reading Notes
+
+Read papers from the Zotero collection "$collection" and create or update detailed reading notes.
+
+## Default target
+
+- **Preferred target**: the bound Obsidian project knowledge base (`Sources/Papers/*.md`)
+- **Fallback target**: `reading-notes-{collection}.md` in the working directory if the current repo is not bound to Obsidian
+
+## Workflow
+
+### Step 0: Resolve whether the current repo is Obsidian-bound
+
+1. If `.claude/project-memory/registry.yaml` exists for the current repo, treat the bound vault as the primary output target.
+2. If the repo is a research project but not yet bound, bootstrap it first.
+3. If there is no bound project context, fall back to a plain markdown output in the working directory.
+4. Treat this command as an explicit agent-first ingestion pass under `$zotero-obsidian-bridge`.
+
+### Step 1: Load papers from Zotero
+
+1. Call `mcp__zotero__zotero_get_collections` to find the matching collection.
+2. Call `mcp__zotero__zotero_get_collection_items` to list the papers.
+3. For each item, call:
+   - `mcp__zotero__zotero_get_item_metadata`
+   - `mcp__zotero__zotero_get_item_fulltext` when a PDF is available
+   - `mcp__zotero__zotero_get_annotations` when helpful
+   - `mcp__zotero__zotero_get_notes` when helpful
+4. If MCP transport fails but a local `zotero-mcp` checkout is available, use the local Python fallback instead of stopping the pass.
+5. Treat Zotero `webpage` items as weak-source inputs unless they clearly expose full paper metadata and useful full text. Abstract-only or placeholder pages must stay `To-Read` and cannot support `Knowledge` or `Writing` claims.
+
+### Step 2: Create/update the canonical paper note
+
+If the project is Obsidian-bound, create or update one canonical note per paper under `Sources/Papers/`.
+
+Each detailed note should contain:
+- `Claim`
+- `Research question`
+- `Method`
+- `Evidence`
+- `Strengths`
+- `Limitation`
+- `Direct relevance to repo`
+- `Relation to other papers`
+- `Knowledge links`
+- `Optional downstream hooks`
+- canonical `Evidence Record` with `Source type` and `Claim strength` when the paper has reusable claims
+
+Recommended frontmatter fields:
+- `title`, `authors`, `year`, `venue`, `doi`, `url`, `citekey`, `zotero_key`
+- `keywords`, `concepts`, `methods`
+- `related_papers`, `linked_knowledge`, `argument_claims`, `argument_methods`, `argument_gaps`, `paper_relationships`
+
+Prefer updating the existing note over creating a sibling note.
+
+### Step 3: Collection coverage and synthesis
+
+After the paper-note pass:
+- update a collection inventory note when the source is a named collection
+- record item -> canonical note mapping and coverage counts such as `16 / 16`
+- verify coverage against expected Zotero keys, DOI values, or arXiv IDs when the user supplied them
+- label abstract-only and webpage-placeholder items separately in the inventory
+- synthesize durable literature knowledge under `Knowledge/`, for example:
+  - `Knowledge/Literature Overview.md`
+  - `Knowledge/Method Taxonomy.md`
+  - `Knowledge/Research Gaps.md`
+
+Prefer updating existing canonical knowledge notes over creating parallel summaries.
+
+### Step 4: Refresh the default literature canvas
+
+After batch note creation or substantial note updates, refresh:
+
+```bash
+python3 "${CLAUDE_PLUGIN_ROOT}/skills/obsidian-literature-workflow/scripts/build_literature_canvas.py" --cwd "$PWD"
+```
+
+This rebuilds `Maps/literature.canvas` from paper-note and knowledge-note links.
+
+### Step 5: Optional synthesis outputs
+
+- If `format=comparison` and promoted claims pass the evidence gate, also update `Writing/comparison-matrix.md`.
+- If the paper batch already supports a thematic synthesis and promoted claims pass the evidence gate, update `Writing/related-work-draft.md`.
+  If not, write only a coverage warning or claim map.
+
+### Step 6: Minimal write-back
+
+Always update:
+- today's `Daily/YYYY-MM-DD.md`
+- repo-local binding summary when project state changes
+
+### Step 7: Final response
+
+Include:
+- collection size and coverage summary
+- created / updated note paths
+- optional `obsidian://open` links
+- optional `obsidian open ...` suggestions when CLI is available
+
+## Fallback behavior
+
+If the repo is not bound to Obsidian:
+- create `reading-notes-{collection}.md`
+- if `format=comparison` and promoted claims pass the evidence gate, also create `comparison-matrix.md`
+
+## Notes
+
+- Zotero remains the source of truth for collection structure, metadata, attachments, PDF full text, and annotations.
+- Obsidian remains the durable project knowledge surface for reading notes, project relevance, and cross-note linking.
+- Default bridge targets are `Sources/Papers/` and `Knowledge/`.
+- Do not dump raw full text into Obsidian paper notes.
+- Do not create `Concepts/` or `Datasets/` trees by default.
+- Refresh `Maps/literature.canvas` by default after a substantial Zotero ingestion pass.
+- Treat `Experiments/` and `Results/` as later project workflows, not the default Zotero-import destination.
+- Do not let abstract-only or webpage-placeholder items support durable claims.