docs: add external documentation site content

Add structured documentation covering quickstart, architecture, core
concepts, API reference, adapter guides, CLI commands, deployment
options, and operator/developer guides.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs/cli/setup-commands.md

@@ -0,0 +1,102 @@
+---
+title: Setup Commands
+summary: Onboard, run, doctor, and configure
+---
+
+# Setup Commands
+
+Instance setup and diagnostics commands.
+
+## `paperclip run`
+
+One-command bootstrap and start:
+
+```sh
+pnpm paperclip run
+```
+
+Does:
+
+1. Auto-onboards if config is missing
+2. Runs `paperclip doctor` with repair enabled
+3. Starts the server when checks pass
+
+Choose a specific instance:
+
+```sh
+pnpm paperclip run --instance dev
+```
+
+## `paperclip onboard`
+
+Interactive first-time setup:
+
+```sh
+pnpm paperclip onboard
+```
+
+Prompts for:
+
+1. Deployment mode (`local_trusted` or `authenticated`)
+2. Exposure policy (if authenticated: `private` or `public`)
+3. Public URL (if authenticated + public)
+4. Database and secrets configuration
+
+## `paperclip doctor`
+
+Health checks with optional auto-repair:
+
+```sh
+pnpm paperclip doctor
+pnpm paperclip doctor --repair
+```
+
+Validates:
+
+- Server configuration
+- Database connectivity
+- Secrets adapter configuration
+- Storage configuration
+- Missing key files
+
+## `paperclip configure`
+
+Update configuration sections:
+
+```sh
+pnpm paperclip configure --section server
+pnpm paperclip configure --section secrets
+pnpm paperclip configure --section storage
+```
+
+## `paperclip env`
+
+Show resolved environment configuration:
+
+```sh
+pnpm paperclip env
+```
+
+## `paperclip allowed-hostname`
+
+Allow a private hostname for authenticated/private mode:
+
+```sh
+pnpm paperclip allowed-hostname my-tailscale-host
+```
+
+## Local Storage Paths
+
+| Data | Default Path |
+|------|-------------|
+| Config | `~/.paperclip/instances/default/config.json` |
+| Database | `~/.paperclip/instances/default/db` |
+| Logs | `~/.paperclip/instances/default/logs` |
+| Storage | `~/.paperclip/instances/default/data/storage` |
+| Secrets key | `~/.paperclip/instances/default/secrets/master.key` |
+
+Override with:
+
+```sh
+PAPERCLIP_HOME=/custom/home PAPERCLIP_INSTANCE_ID=dev pnpm paperclip run
+```