claude-second-brain 0.5.1 → 1.0.0

package/README.md

@@ -58,26 +58,27 @@ Everything is pre-configured. You bring the sources.
 npx claude-second-brain
 ```
 
+Or install globally — `csb` is a shorter alias:
+
+```bash
+npm i -g claude-second-brain
+csb
+```
+
 The CLI will ask:
-- **Folder name** — where to create your vault (default: `my-brain`)
-- **qmd index path** — where to store the local search index (default: `~/.cache/qmd/index.sqlite`)
+- **Brain name** — what to call this brain (default: `my-brain`)
 - **GitHub repo** — optionally create a private repo and push automatically (requires `gh` CLI)
 
-Then scaffolds the vault, installs `mise` + `node` + `pnpm`, runs `pnpm install`, and `git init`.
+Creates the brain at `~/.claude-second-brain/my-brain/`, registers it in `~/.claude-second-brain/config.toml`, installs `mise` + `node` + `pnpm`, runs `pnpm install`, and `git init`.
 
-**Step 2 — Initialize inside Claude Code**
+**Step 2 — Generate vector embeddings**
 
 ```bash
-cd my-brain && claude
+cd ~/.claude-second-brain/my-brain
+pnpm qmd:reindex
 ```
 
-Then run:
-
-```
-/setup
-```
-
-Registers the qmd collections and generates local vector embeddings. First run downloads ~2GB of GGUF models — once.
+First run downloads ~2GB of GGUF models — once per machine. qmd collections are already registered by the CLI during scaffolding.
 
 **Step 3 — Open in Obsidian (and push to GitHub if not done)**
 
@@ -90,7 +91,7 @@ git remote add origin https://github.com/you/my-brain.git
 git push -u origin main
 ```
 
-Open `my-brain/` as a vault in Obsidian — the folder is already a valid Obsidian vault. The Git plugin is pre-configured — enable it and sync is automatic.
+Open `~/.claude-second-brain/my-brain/` as a vault in Obsidian — the folder is already a valid Obsidian vault. The Git plugin is pre-configured — enable it and sync is automatic.
 
 ---
 
@@ -112,10 +113,6 @@ The wiki ships with a set of slash commands that cover the full workflow. No man
 
 **`/brain-rebuild`** — **Destructive.** Redesigns the qmd schema: analyzes the wiki, proposes new collections and contexts, waits for your approval, then patches `scripts/qmd/setup.ts`, drops the old index, and rebuilds embeddings from scratch. Use only when the current structure no longer fits how you search.
 
-### Setup
-
-**`/setup`** — First-time initialization. Registers the qmd collections and generates local vector embeddings. Run once after scaffolding.
-
 ---
 
 ## Access from anywhere
@@ -223,34 +220,53 @@ All pages cross-link with Obsidian `[[wikilinks]]`. Contradictions are flagged w
 
 ## Directory layout
 
+All brains live under `~/.claude-second-brain/`. A central `config.toml` tracks them.
+
 ```
-my-brain/
-├── CLAUDE.md              ← The schema. Claude reads this every session.
-├── raw-sources/           ← Your raw inputs. Claude never modifies these.
-│   ├── articles/
-│   ├── pdfs/
-│   └── personal/
-├── wiki/                  ← Claude owns this entirely.
-│   ├── index.md
-│   ├── log.md
-│   ├── overview.md
-│   ├── sources/
-│   └── qa/
-└── scripts/qmd/           ← Semantic search setup and re-indexing
+~/.claude-second-brain/
+├── config.toml            ← Brain registry (default brain, paths, git remotes)
+└── my-brain/
+    ├── CLAUDE.md          ← The schema. Claude reads this every session.
+    ├── raw-sources/       ← Your raw inputs. Claude never modifies these.
+    │   ├── articles/
+    │   ├── pdfs/
+    │   └── personal/
+    ├── wiki/              ← Claude owns this entirely.
+    │   ├── index.md
+    │   ├── log.md
+    │   ├── overview.md
+    │   ├── sources/
+    │   └── qa/
+    ├── scripts/qmd/       ← Semantic search setup and re-indexing
+    └── .qmd/              ← qmd index (gitignored)
+```
+
+## Multiple brains
+
+Run `npx claude-second-brain` again to create additional brains. Each gets its own folder, its own qmd index, and its own git remote — fully isolated. The global skills (`/brain-ingest`, `/brain-search`, `/brain-refresh`) always operate on the **default brain** declared in `config.toml`. The first brain you create is set as the default automatically.
+
+Manage brains from the CLI:
+
+```bash
+npx claude-second-brain ls                  # list all brains (default marked with *)
+npx claude-second-brain rm <name>           # remove a brain (deletes its folder + config entry)
+npx claude-second-brain path                # print the default brain's directory
+npx claude-second-brain path --qmd          # print the default brain's qmd index path
+npx claude-second-brain qmd -- query -c wiki "<terms>"   # run qmd against the default brain
 ```
 
 ---
 
 ## Installing and updating skills
 
-Skills are slash commands Claude Code loads from `.claude/skills/[name]/SKILL.md`. `/brain-ingest`, `/brain-search`, and `/brain-refresh` install globally to `~/.claude/skills/` during setup so they work in any Claude Code session. `/brain-rebuild`, `/lint`, `/setup`, and `/qmd-cli` live inside the vault at `.claude/skills/`.
+Skills are slash commands Claude Code loads from `.claude/skills/[name]/SKILL.md`. `/brain-ingest`, `/brain-search`, and `/brain-refresh` install globally to `~/.claude/skills/` during setup so they work in any Claude Code session. `/brain-rebuild` and `/lint` live inside the vault at `.claude/skills/`.
 
 ### Update the built-in wiki skills
 
 The wiki's own skills are scaffolded at creation time. To pull in improvements, use `npx skills` pointing to the template skills directory in this repo:
 
 ```bash
-# Install or update all 7 wiki skills from the latest template
+# Install or update all 5 wiki skills from the latest template
 npx skills add https://github.com/jessepinkman9900/claude-second-brain/tree/main/template/.claude/skills -a claude-code -y
 
 # Or update a specific skill