claude-second-brain 0.4.1 → 0.5.1

package/README.md

@@ -63,7 +63,7 @@ The CLI will ask:
 - **qmd index path** — where to store the local search index (default: `~/.cache/qmd/index.sqlite`)
 - **GitHub repo** — optionally create a private repo and push automatically (requires `gh` CLI)
 
-Then scaffolds the vault, installs `mise` + `bun`, and runs `git init`.
+Then scaffolds the vault, installs `mise` + `node` + `pnpm`, runs `pnpm install`, and `git init`.
 
 **Step 2 — Initialize inside Claude Code**
 
@@ -100,7 +100,7 @@ The wiki ships with a set of slash commands that cover the full workflow. No man
 
 ### Daily workflow
 
-**`/brain-ingest`** — Drop a file into `sources/articles/`, `sources/pdfs/`, or `sources/personal/`. Run `/brain-ingest`. Claude summarizes the source, asks what matters most to you, creates a `wiki/sources/` page, updates or creates related topic pages, flags any contradictions with existing knowledge, and logs everything.
+**`/brain-ingest`** — Drop a file into `raw-sources/articles/`, `raw-sources/pdfs/`, or `raw-sources/personal/`. Run `/brain-ingest`. Claude summarizes the source, asks what matters most to you, creates a `wiki/sources/` page, updates or creates related topic pages, flags any contradictions with existing knowledge, and logs everything.
 
 **`/brain-search`** — Ask anything about what you know. Claude runs hybrid semantic search across the wiki, reads the most relevant pages, and writes an answer with inline `[[wiki/page]]` citations. If the answer synthesizes multiple pages in a novel way, it offers to file it as a permanent `wiki/qa/` entry.
 
@@ -137,7 +137,7 @@ Sources flow in on the left, Claude synthesizes them into the wiki, qmd indexes
 
 ```mermaid
 flowchart TB
-  subgraph Sources["sources/ — raw, immutable"]
+  subgraph Sources["raw-sources/ — raw, immutable"]
     direction LR
     S1[articles/]
     S2[pdfs/]
@@ -226,7 +226,7 @@ All pages cross-link with Obsidian `[[wikilinks]]`. Contradictions are flagged w
 ```
 my-brain/
 ├── CLAUDE.md              ← The schema. Claude reads this every session.
-├── sources/               ← Your raw inputs. Claude never modifies these.
+├── raw-sources/           ← Your raw inputs. Claude never modifies these.
 │   ├── articles/
 │   ├── pdfs/
 │   └── personal/

package/bin/create.js

@@ -173,13 +173,19 @@ async function main() {
     else spin.stop("Failed to install mise — run: npm install -g @jdxcode/mise", 1)
   }
 
-  // Run mise install inside the new vault to install bun
-  spin.start("Installing bun via mise")
+  // Run mise install inside the new vault to install node + pnpm
+  spin.start("Installing node + pnpm via mise")
   run(["mise", "trust"], targetDir)
   const miseOk = run(["mise", "install"], targetDir)
-  if (miseOk) spin.stop("bun installed")
+  if (miseOk) spin.stop("node + pnpm installed")
   else spin.stop("mise install failed — run it manually inside your vault", 1)
 
+  // Install vault dependencies via pnpm
+  spin.start("Installing vault dependencies")
+  const pnpmOk = run(["mise", "exec", "--", "pnpm", "install"], targetDir)
+  if (pnpmOk) spin.stop("dependencies installed")
+  else spin.stop("pnpm install failed — run it manually inside your vault", 1)
+
   // Git init
   spin.start("Initializing git repo")
   const gitOk = run(["git", "init"], targetDir)

package/package.json

@@ -1,19 +1,25 @@
 {
   "name": "claude-second-brain",
-  "version": "0.4.1",
-  "description": "Scaffold an LLM-maintained Obsidian knowledge wiki",
+  "version": "0.5.1",
+  "description": "The fastest way to start your personal knowledge base powered by Obsidian, Claude Code, qmd, and GitHub.",
   "type": "module",
   "bin": {
     "claude-second-brain": "./bin/create.js"
   },
+  "scripts": {
+    "docs:dev": "vocs dev",
+    "docs:build": "vocs build",
+    "docs:preview": "vocs preview"
+  },
   "files": [
     "bin/",
     "template/",
     "image.png"
   ],
   "engines": {
-    "node": ">=18.0.0"
+    "node": ">=22.0.0"
   },
+  "packageManager": "pnpm@10.8.0",
   "dependencies": {
     "@clack/prompts": "^1.2.0",
     "picocolors": "^1.1.1"
@@ -22,5 +28,12 @@
   "repository": {
     "type": "git",
     "url": "https://github.com/jessepinkman9900/claude-second-brain"
+  },
+  "devDependencies": {
+    "@types/react": "^19.2.14",
+    "react": "^19.2.5",
+    "react-dom": "^19.2.5",
+    "typescript": "^6.0.2",
+    "vocs": "1.4.1"
   }
 }

package/template/.claude/skills/brain-ingest/SKILL.md

@@ -1,7 +1,7 @@
 ---
 name: brain-ingest
 description: "Ingest a new source into the wiki. Reads the source, summarizes it, creates a wiki/sources/ page, updates affected topic and entity pages, flags contradictions, and logs the activity. Trigger phrases: /brain-ingest, ingest [file or URL], add this source, read and file this, process this article/paper/note."
-argument-hint: "File path (e.g. sources/articles/my-article.md), URL, or leave blank if source is pasted in chat"
+argument-hint: "File path (e.g. raw-sources/articles/my-article.md), URL, or leave blank if source is pasted in chat"
 ---
 
 # Brain Ingest
@@ -10,7 +10,7 @@ Runs the full 9-step ingest workflow defined in CLAUDE.md. Do not skip steps.
 
 ## Inputs
 
-- **File path** — a file in `sources/articles/`, `sources/pdfs/`, or `sources/personal/`
+- **File path** — a file in `raw-sources/articles/`, `raw-sources/pdfs/`, or `raw-sources/personal/`
 - **URL** — fetch and read the full content directly
 - **Pasted text** — treat whatever the user has shared as the source
 
@@ -35,7 +35,7 @@ Runs the full 9-step ingest workflow defined in CLAUDE.md. Do not skip steps.
 - Add the new source to the Sources Ingested section: one-line description + `[[wiki/sources/slug]]` link
 
 **Step 5 — Identify affected wiki pages**
-- Run: `INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd query -c wiki "<source topic and key claims>"`
+- Run: `INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd query -c wiki "<source topic and key claims>"`
 - Also Glob `wiki/*.md` and `wiki/sources/*.md` to catch anything qmd missed
 - List all pages to create or update before proceeding
 
@@ -63,6 +63,6 @@ Runs the full 9-step ingest workflow defined in CLAUDE.md. Do not skip steps.
 
 ## Hard Rules
 
-- Never modify anything in `sources/` — immutable raw inputs
+- Never modify anything in `raw-sources/` — immutable raw inputs
 - Every wiki page must have frontmatter with at least `type` and `updated`
 - One source summary page per source — never merge two sources into one

package/template/.claude/skills/brain-rebuild/SKILL.md

@@ -12,7 +12,7 @@ Redesigns the qmd schema based on what the wiki actually contains today, then re
 
 - The wiki has grown and the current single `wiki` collection no longer matches how the user searches
 - The user wants finer-grained contexts (e.g. distinct context descriptions per sub-folder)
-- After significant reorganization of `wiki/` or `sources/` folder structure
+- After significant reorganization of `wiki/` or `raw-sources/` folder structure
 - Never as a routine refresh — for that, use `/brain-refresh`
 
 ## Procedure
@@ -25,14 +25,14 @@ All commands run from the vault root.
 - Read `CLAUDE.md` to understand the documented schema and any references to collection names
 - List current state from qmd:
   ```bash
-  INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd collection list
-  INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd context list
-  INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd status
+  INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd collection list
+  INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd context list
+  INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd status
   ```
 
 ### Step 2 — Analyze the wiki
 
-- Glob `wiki/**/*.md` and `sources/**/*.md`
+- Glob `wiki/**/*.md` and `raw-sources/**/*.md`
 - Read enough pages (especially `wiki/index.md` and `wiki/overview.md`) to understand actual topic clusters, page-type distribution, and folder structure
 - Identify natural groupings: by domain (e.g. ml, distributed-systems, finance), by page type (topics vs entities vs qa), by source provenance, etc.
 
@@ -74,20 +74,20 @@ If collection names changed:
 For each existing collection that no longer fits the new schema:
 
 ```bash
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd collection remove <old-name>
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd collection remove <old-name>
 ```
 
 For each obsolete context:
 
 ```bash
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd context rm <path>
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd context rm <path>
 ```
 
 ### Step 8 — Register the new schema
 
 Run:
 ```bash
-bun scripts/qmd/setup.ts
+pnpm qmd:setup
 ```
 
 This is idempotent — collections that already exist (e.g. ones you kept) are skipped; new ones are added; contexts are upserted.
@@ -96,7 +96,7 @@ This is idempotent — collections that already exist (e.g. ones you kept) are s
 
 Run:
 ```bash
-bun scripts/qmd/reindex.ts
+pnpm qmd:reindex
 ```
 
 This indexes all files under the new collections and generates fresh embeddings.
@@ -104,9 +104,9 @@ This indexes all files under the new collections and generates fresh embeddings.
 ### Step 10 — Verify and report
 
 ```bash
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd collection list
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd context list
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd status
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd collection list
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd context list
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd status
 ```
 
 Confirm the new collections appear, contexts match the plan, and document/embedding counts are non-zero. Report a summary of what changed (collections added/removed/renamed, contexts updated, files re-indexed, references updated in CLAUDE.md and skills).
@@ -116,4 +116,4 @@ Confirm the new collections appear, contexts match the plan, and document/embedd
 - Never apply schema changes without explicit user approval at Step 4
 - Never delete a collection without first showing the user what will be dropped
 - Always update `CLAUDE.md` and skill files in lockstep with collection renames — stale `-c <name>` references will silently break `/brain-search`
-- Do not touch `wiki/`, `sources/`, or any user content — this skill changes the index schema, not the data
+- Do not touch `wiki/`, `raw-sources/`, or any user content — this skill changes the index schema, not the data

package/template/.claude/skills/brain-refresh/SKILL.md

@@ -6,12 +6,12 @@ argument-hint: "Optional: 'force' to force re-embedding of every chunk (slow, us
 
 # Brain Refresh
 
-Refreshes the qmd index so search reflects the current state of the vault. Wraps `bun scripts/qmd/reindex.ts` (incremental) and the qmd CLI's force-embed flag.
+Refreshes the qmd index so search reflects the current state of the vault. Wraps `pnpm qmd:reindex` (incremental) and the qmd CLI's force-embed flag.
 
 ## When to Use
 
 - After a `/brain-ingest` session (or several) — batch the refresh, don't run after every file edit
-- After manual edits to `wiki/` or `sources/` files
+- After manual edits to `wiki/` or `raw-sources/` files
 - When `/brain-search` results feel stale or miss recently added content
 - After upgrading `@tobilu/qmd` or changing the embedding model — use `force` mode
 
@@ -23,7 +23,7 @@ All commands run from the vault root.
 
 Run:
 ```bash
-bun scripts/qmd/reindex.ts
+pnpm qmd:reindex
 ```
 
 This script does two things:
@@ -38,10 +38,10 @@ When the user passes `force`, re-embed **every** chunk — not just the changed
 
 ```bash
 # Step 1 — update the file index first
-bun scripts/qmd/reindex.ts
+pnpm qmd:reindex
 
 # Step 2 — force re-embed everything
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd embed -f
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd embed -f
 ```
 
 Force mode is slow — confirm with the user before proceeding if the wiki is large.
@@ -51,7 +51,7 @@ Force mode is slow — confirm with the user before proceeding if the wiki is la
 After refresh, confirm with:
 
 ```bash
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd status
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd status
 ```
 
 Document and embedding counts should be non-zero and reflect recent activity. If embeddings show as `0` or far below document count, re-run the refresh.

package/template/.claude/skills/brain-search/SKILL.md

@@ -11,7 +11,7 @@ Runs the 4-step query workflow defined in CLAUDE.md. Answers come with inline `[
 ## Workflow
 
 **Step 1 — Search the wiki**
-- Run hybrid search: `INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd query -c wiki "<question>"`
+- Run hybrid search: `INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd query -c wiki "<question>"`
 - Read `wiki/index.md` to confirm coverage and catch any pages qmd didn't surface
 - Read the 2–5 most relevant pages in full before synthesizing
 

package/template/.claude/skills/qmd-cli/SKILL.md

@@ -13,10 +13,10 @@ Local semantic document index with hybrid search (BM25 + vector), collection man
 This vault keeps its index at `__QMD_PATH__`. All CLI commands **must** prefix with `INDEX_PATH=__QMD_PATH__`:
 
 ```bash
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd query -c wiki "..."
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd query -c wiki "..."
 ```
 
-The scripts `bun scripts/qmd/setup.ts` and `bun scripts/qmd/reindex.ts` write to this same file. The CLI must match.
+The scripts `pnpm qmd:setup` and `pnpm qmd:reindex` write to this same file. The CLI must match.
 
 ---
 
@@ -24,40 +24,40 @@ The scripts `bun scripts/qmd/setup.ts` and `bun scripts/qmd/reindex.ts` write to
 
 ```bash
 # Create/index a collection
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd collection add <path> --name <name> --mask <glob-pattern>
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd collection add <path> --name <name> --mask <glob-pattern>
 # e.g.:
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd collection add wiki --name wiki --mask "**/*.md"
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd collection add wiki --name wiki --mask "**/*.md"
 
 # List all collections with details
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd collection list
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd collection list
 
 # Remove a collection
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd collection remove <name>
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd collection remove <name>
 
 # Rename a collection
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd collection rename <old-name> <new-name>
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd collection rename <old-name> <new-name>
 ```
 
 ## Listing Files
 
 ```bash
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd ls
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd ls [collection[/path]]
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd ls
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd ls [collection[/path]]
 ```
 
 ## Context
 
 ```bash
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd context add [path] "description text"
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd context list
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd context rm <path>
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd context add [path] "description text"
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd context list
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd context rm <path>
 ```
 
 ## Retrieving Documents
 
 ```bash
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd get <file>[:line] [-l N] [--from N]
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd multi-get <pattern> [-l N] [--max-bytes N]
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd get <file>[:line] [-l N] [--from N]
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd multi-get <pattern> [-l N] [--max-bytes N]
 ```
 
 **Multi-get format flags:** `--json`, `--csv`, `--md`, `--xml`, `--files`
@@ -66,16 +66,16 @@ INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd multi-get <pattern> [-l N] [--max-bytes
 
 ```bash
 # Show index status and collections
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd status
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd status
 
 # Re-index all collections
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd update [--pull]
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd update [--pull]
 
 # Create vector embeddings (900 tokens/chunk, 15% overlap)
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd embed [-f]
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd embed [-f]
 
 # Remove cache and orphaned data, vacuum DB
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd cleanup
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd cleanup
 ```
 
 > After bulk ingest sessions, run `update` then `embed` to keep the index fresh.
@@ -108,28 +108,28 @@ INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd cleanup
 
 ```bash
 # Hybrid search across all collections
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd query "distributed systems consensus"
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd query "distributed systems consensus"
 
 # Search only the wiki collection, JSON output
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd query -c wiki "transformer architecture" --json
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd query -c wiki "transformer architecture" --json
 
 # Keyword-only search, top 10, markdown output
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd search -c wiki "kafka" -n 10 --md
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd search -c wiki "kafka" -n 10 --md
 
 # Vector search with full documents
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd vsearch "attention mechanism" --full
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd vsearch "attention mechanism" --full
 
 # Filter by score threshold
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd query "machine learning" --all --min-score 0.7
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd query "machine learning" --all --min-score 0.7
 ```
 
 ## MCP Server
 
 ```bash
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd mcp
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd mcp --http [--port N]
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd mcp --http --daemon
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd mcp stop
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd mcp
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd mcp --http [--port N]
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd mcp --http --daemon
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd mcp stop
 ```
 
 ## Global Options
@@ -145,24 +145,24 @@ Note: use `INDEX_PATH` env var rather than `--index` — `INDEX_PATH` accepts a
 ### First-time setup for this vault
 ```bash
 # Handled by the /setup skill:
-bun scripts/qmd/setup.ts
-bun scripts/qmd/reindex.ts
+pnpm qmd:setup
+pnpm qmd:reindex
 ```
 
 ### After a bulk ingest session
 ```bash
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd update
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd embed
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd update
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd embed
 ```
 
 ### Research workflow
 ```bash
 # Discover relevant pages
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd query -c wiki "<topic>"
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd query -c wiki "<topic>"
 
 # Get a specific file
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd get wiki/distributed-systems.md
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd get wiki/distributed-systems.md
 
 # Get multiple related files
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd multi-get "wiki/kafka.md,wiki/distributed-systems.md" --md
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd multi-get "wiki/kafka.md,wiki/distributed-systems.md" --md
 ```

package/template/.claude/skills/setup/SKILL.md

@@ -21,7 +21,7 @@ All commands run from the vault root.
 
 Run:
 ```bash
-bun scripts/qmd/setup.ts
+pnpm qmd:setup
 ```
 
 Registers the two core qmd collections (`wiki`, `raw-sources`) and their path-level context descriptions. Idempotent — safe to re-run.
@@ -30,7 +30,7 @@ Registers the two core qmd collections (`wiki`, `raw-sources`) and their path-le
 
 Run:
 ```bash
-bun scripts/qmd/reindex.ts
+pnpm qmd:reindex
 ```
 
 Scans all collections for new/changed files and generates vector embeddings. The first run downloads ~2GB of local GGUF models — this will take a while.
@@ -39,7 +39,7 @@ Scans all collections for new/changed files and generates vector embeddings. The
 
 Skip step 1 and run only:
 ```bash
-bun scripts/qmd/reindex.ts
+pnpm qmd:reindex
 ```
 
 Do **not** re-run after every single file edit — batch it after a session.
@@ -50,17 +50,17 @@ Run these three commands to confirm everything is working:
 
 ```bash
 # List registered collections (expect: wiki, raw-sources)
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd collection list
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd collection list
 
 # List registered contexts
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd context list
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd context list
 
 # Show index status and embedding counts
-INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd status
+INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd status
 ```
 
 Both collections should appear in `collection list`. `status` should show non-zero document and embedding counts — if embeddings are 0, re-run step 2.
 
 ## Notes
-- `bun` is managed via `mise` — ensure `mise install` has been run before setup
-- If `bunx @tobilu/qmd` commands fail after setup, re-run step 1 then step 2
+- `node` and `pnpm` are managed via `mise` — ensure `mise install` and `pnpm install` have been run before setup
+- If `pnpm dlx @tobilu/qmd` commands fail after setup, re-run step 1 then step 2

package/template/CLAUDE.md

@@ -18,7 +18,7 @@ Claude is responsible for: summarizing, cross-referencing, filing, and maintaini
 ```
 claude-second-brain/
 ├── CLAUDE.md              ← This file. The schema.
-├── sources/               ← Raw source material. IMMUTABLE — Claude never modifies these.
+├── raw-sources/           ← Raw source material. IMMUTABLE — Claude never modifies these.
 │   ├── articles/          ← Web articles saved as markdown
 │   ├── pdfs/              ← PDF files or extracted text
 │   └── personal/          ← Personal notes flagged for ingestion
@@ -95,7 +95,7 @@ Run this workflow whenever the user adds a new source. Do not skip steps.
 
 **Step 1 — Read the source**
 - If URL: fetch and read the full content.
-- If file in `sources/`: read it with the Read tool.
+- If file in `raw-sources/`: read it with the Read tool.
 - If pasted text: treat as the source.
 
 **Step 2 — Discuss with the user**
@@ -111,7 +111,7 @@ Run this workflow whenever the user adds a new source. Do not skip steps.
 - Add the new source to the Sources section with a one-line description and link.
 
 **Step 5 — Identify affected wiki pages**
-- Run `INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd query -c wiki "<source topic and key claims>"` to surface related existing wiki pages.
+- Run `INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd query -c wiki "<source topic and key claims>"` to surface related existing wiki pages.
 - Also Glob `wiki/*.md` and `wiki/sources/*.md` to ensure completeness.
 - List all pages to create or update.
 
@@ -142,7 +142,7 @@ Run this workflow whenever the user adds a new source. Do not skip steps.
 Run this workflow when the user asks a question against the wiki.
 
 **Step 1 — Search the wiki**
-- Run `INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd query -c wiki "<question>"` to surface semantically relevant pages.
+- Run `INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd query -c wiki "<question>"` to surface semantically relevant pages.
 - Read `wiki/index.md` to confirm coverage and catch any pages qmd didn't surface.
 - Read the 2-5 most relevant pages fully.
 
@@ -199,7 +199,7 @@ N issues found, N fixed. [Brief summary of notable findings.]
 
 ## Hard Rules
 
-1. **Never modify anything in `sources/`**. These are immutable raw inputs.
+1. **Never modify anything in `raw-sources/`**. These are immutable raw inputs.
 2. **Never touch existing vault files** (daily-notes, misc, ideas, root-level .md files, .obsidian/). The wiki lives only in `wiki/`.
 3. **Always append to `wiki/log.md`** — never overwrite it.
 4. **One source summary per ingested source** in `wiki/sources/`. Never merge two sources into one summary page.
@@ -211,21 +211,21 @@ N issues found, N fixed. [Brief summary of notable findings.]
 
 ## Search Tool
 
-This vault uses **qmd** (`bunx @tobilu/qmd`) for local semantic and full-text search.
-Collections and contexts are registered via `bun scripts/qmd/setup.ts` and stored at `__QMD_PATH__` (gitignored).
+This vault uses **qmd** (`pnpm dlx @tobilu/qmd`) for local semantic and full-text search.
+Collections and contexts are registered via `pnpm qmd:setup` and stored at `__QMD_PATH__` (gitignored).
 
 Key commands:
 
 | Command | Use |
 |---------|-----|
-| `INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd query -c wiki "<question>"` | Hybrid search — best for topic discovery |
-| `INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd search -c wiki "<terms>"` | Fast keyword search (BM25, no LLM) |
-| `INDEX_PATH=__QMD_PATH__ bunx @tobilu/qmd vsearch -c wiki "<question>"` | Pure vector/semantic search |
+| `INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd query -c wiki "<question>"` | Hybrid search — best for topic discovery |
+| `INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd search -c wiki "<terms>"` | Fast keyword search (BM25, no LLM) |
+| `INDEX_PATH=__QMD_PATH__ pnpm dlx @tobilu/qmd vsearch -c wiki "<question>"` | Pure vector/semantic search |
 
 Add `--json` for structured output. Omit `-c wiki` to search all collections (wiki, raw-sources, human, daily-notes).
 
 **Re-indexing:** After a bulk ingest session run:
 ```bash
-bun scripts/qmd/reindex.ts
+pnpm qmd:reindex
 ```
 Do NOT re-index after every single file edit.

package/template/README.md

@@ -13,10 +13,13 @@ Inspired by [Andrej Karpathy's approach to LLM-powered knowledge management](htt
 ## Quick start
 
 ```bash
-# 1. Install tools
+# 1. Install tools (node + pnpm via mise)
 mise install
 
-# 2. Open Claude Code
+# 2. Install dependencies
+pnpm install
+
+# 3. Open Claude Code
 claude
 ```
 
@@ -36,7 +39,7 @@ Registers the qmd collections and generates local vector embeddings. First run d
 
 ### Daily workflow
 
-**`/brain-ingest`** — Add a file to `sources/articles/`, `sources/pdfs/`, or `sources/personal/`, then run `/brain-ingest`. Claude summarizes the source, asks what aspects matter most, updates related wiki pages, flags contradictions, and logs everything.
+**`/brain-ingest`** — Add a file to `raw-sources/articles/`, `raw-sources/pdfs/`, or `raw-sources/personal/`, then run `/brain-ingest`. Claude summarizes the source, asks what aspects matter most, updates related wiki pages, flags contradictions, and logs everything.
 
 **`/brain-search`** — Ask anything: `what do I know about [topic]?` Claude searches the wiki semantically and returns a cited answer. If it synthesizes multiple pages in a useful way, it offers to file it as a permanent `wiki/qa/` entry.
 
@@ -60,7 +63,7 @@ Sources flow in on the left, Claude synthesizes them into the wiki, qmd indexes
 
 ```mermaid
 flowchart TB
-  subgraph Sources["sources/ — raw, immutable"]
+  subgraph Sources["raw-sources/ — raw, immutable"]
     direction LR
     S1[articles/]
     S2[pdfs/]
@@ -138,7 +141,7 @@ All pages cross-link with Obsidian `[[wikilinks]]`. Contradictions are flagged w
 ```
 claude-second-brain/
 ├── CLAUDE.md              ← The schema. Claude reads this every session.
-├── sources/               ← Your raw inputs. Claude never modifies these.
+├── raw-sources/           ← Your raw inputs. Claude never modifies these.
 │   ├── articles/          ← Web articles saved as markdown
 │   ├── pdfs/              ← PDFs or extracted text
 │   └── personal/          ← Brain dumps, rough notes
@@ -185,7 +188,7 @@ After a bulk ingest session, re-index to keep search current:
 /brain-refresh
 ```
 
-This wraps `bun scripts/qmd/reindex.ts` — you can also run that command directly if you're not inside Claude Code. Pass `force` to `/brain-refresh` to re-embed every chunk (e.g. after changing the embedding model).
+This wraps `pnpm qmd:reindex` — you can also run that command directly if you're not inside Claude Code. Pass `force` to `/brain-refresh` to re-embed every chunk (e.g. after changing the embedding model).
 
 ---
 

package/template/mise.toml

@@ -1,2 +1,3 @@
 [tools]
-bun = "1.3.10"
+node = "22"
+pnpm = "10.8.0"

package/template/package.json

@@ -0,0 +1,33 @@
+{
+  "name": "claude-second-brain-vault",
+  "private": true,
+  "type": "module",
+  "scripts": {
+    "qmd:setup": "tsx scripts/qmd/setup.ts",
+    "qmd:reindex": "tsx scripts/qmd/reindex.ts"
+  },
+  "dependencies": {
+    "@tobilu/qmd": "^2.1.0"
+  },
+  "devDependencies": {
+    "@types/node": "^22.10.2",
+    "tsx": "^4.19.2",
+    "typescript": "^5.7.2"
+  },
+  "packageManager": "pnpm@10.8.0",
+  "engines": {
+    "node": ">=22.0.0"
+  },
+  "pnpm": {
+    "onlyBuiltDependencies": [
+      "better-sqlite3",
+      "esbuild",
+      "node-llama-cpp",
+      "tree-sitter-go",
+      "tree-sitter-javascript",
+      "tree-sitter-python",
+      "tree-sitter-rust",
+      "tree-sitter-typescript"
+    ]
+  }
+}

package/template/scripts/qmd/reindex.ts

@@ -4,10 +4,10 @@
  * First run downloads ~2GB of GGUF models — expected, one-time.
  *
  * Run from vault root:
- *   bun scripts/qmd/reindex.ts
+ *   pnpm qmd:reindex
  *
  * Suitable as a cronjob:
- *   0 * * * * cd /home/user/my-brain && bun scripts/qmd/reindex.ts
+ *   0 * * * * cd /home/user/my-brain && pnpm qmd:reindex
  */
 
 import { createStore } from "@tobilu/qmd"

package/template/scripts/qmd/setup.ts

@@ -3,16 +3,17 @@
  * Safe to re-run: skips collections that already exist, upserts contexts.
  *
  * Run once from vault root:
- *   bun scripts/qmd/setup.ts
+ *   pnpm qmd:setup
  *
  * After setup, index the vault:
- *   bun scripts/qmd/reindex.ts
+ *   pnpm qmd:reindex
  */
 
 import { createStore } from "@tobilu/qmd"
-import { join } from "path"
+import { dirname, join } from "node:path"
+import { fileURLToPath } from "node:url"
 
-const VAULT = join(import.meta.dir, "../..")
+const VAULT = join(dirname(fileURLToPath(import.meta.url)), "../..")
 const DB = "__QMD_PATH__"
 
 const store = await createStore({ dbPath: DB })
@@ -32,7 +33,7 @@ async function ensureCollection(name: string, relPath: string, pattern: string)
 
 console.log("Collections:")
 await ensureCollection("wiki",        "wiki",        "**/*.md")
-await ensureCollection("raw-sources", "sources",     "**/*.md")
+await ensureCollection("raw-sources", "raw-sources", "**/*.md")
 
 // --- Global context ---
 console.log("\nContexts:")
@@ -47,10 +48,10 @@ await store.addContext("wiki", "",         "LLM-maintained synthesized knowledge
 await store.addContext("wiki", "/sources", "Source summaries — one page per ingested source, with abstract, key claims, and synthesis notes")
 await store.addContext("wiki", "/qa",      "Filed Q&A answers that synthesize multiple wiki pages around a notable question")
 
-// sources/
+// raw-sources/
 await store.addContext("raw-sources", "",          "Raw source material — immutable originals, never modified after ingestion")
 await store.addContext("raw-sources", "/articles", "Web articles saved as markdown")
 await store.addContext("raw-sources", "/pdfs",     "PDF files or their extracted text")
 await store.addContext("raw-sources", "/personal", "Personal notes flagged for wiki ingestion")
 
-console.log("\nSetup complete. Run: bun scripts/qmd/reindex.ts")
+console.log("\nSetup complete. Run: pnpm qmd:reindex")

package/template/scripts/qmd/tsconfig.json

@@ -1,29 +1,19 @@
 {
   "compilerOptions": {
-    // Environment setup & latest features
     "lib": ["ESNext"],
     "target": "ESNext",
-    "module": "Preserve",
+    "module": "NodeNext",
+    "moduleResolution": "NodeNext",
     "moduleDetection": "force",
-    "jsx": "react-jsx",
     "allowJs": true,
 
-    // Bundler mode
-    "moduleResolution": "bundler",
-    "allowImportingTsExtensions": true,
     "verbatimModuleSyntax": true,
     "noEmit": true,
 
-    // Best practices
     "strict": true,
     "skipLibCheck": true,
     "noFallthroughCasesInSwitch": true,
     "noUncheckedIndexedAccess": true,
-    "noImplicitOverride": true,
-
-    // Some stricter flags (disabled by default)
-    "noUnusedLocals": false,
-    "noUnusedParameters": false,
-    "noPropertyAccessFromIndexSignature": false
+    "noImplicitOverride": true
   }
 }

package/template/scripts/qmd/package.json

@@ -1,14 +0,0 @@
-{
-  "name": "qmd",
-  "private": true,
-  "peerDependencies": {
-    "typescript": "^5"
-  },
-  "dependencies": {
-    "@tobilu/qmd": "^2.1.0"
-  },
-  "devDependencies": {
-    "@types/node": "^25.6.0",
-    "@types/bun": "latest"
-  }
-}