fix: restore docs deleted in v0.2.3 release, add Paperclip branding

- Restored docs/ directory that was accidentally deleted by `git add -A`
  in the v0.2.3 release script
- Replaced generic "P" favicon with actual paperclip icon using brand
  primary color (#2563EB)
- Added light/dark logo SVGs for Mintlify navbar (paperclip icon + wordmark)
- Updated docs.json with logo configuration for dark/light mode
- Fixed release.sh to stage only release-related files instead of `git add -A`
  to prevent sweeping unrelated changes into release commits

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

docs/cli/overview.md

@@ -0,0 +1,67 @@
+---
+title: CLI Overview
+summary: CLI installation and setup
+---
+
+The Paperclip CLI handles instance setup, diagnostics, and control-plane operations.
+
+## Usage
+
+```sh
+pnpm paperclipai --help
+```
+
+## Global Options
+
+All commands support:
+
+| Flag | Description |
+|------|-------------|
+| `--data-dir <path>` | Local Paperclip data root (isolates from `~/.paperclip`) |
+| `--api-base <url>` | API base URL |
+| `--api-key <token>` | API authentication token |
+| `--context <path>` | Context file path |
+| `--profile <name>` | Context profile name |
+| `--json` | Output as JSON |
+
+Company-scoped commands also accept `--company-id <id>`.
+
+For clean local instances, pass `--data-dir` on the command you run:
+
+```sh
+pnpm paperclipai run --data-dir ./tmp/paperclip-dev
+```
+
+## Context Profiles
+
+Store defaults to avoid repeating flags:
+
+```sh
+# Set defaults
+pnpm paperclipai context set --api-base http://localhost:3100 --company-id <id>
+
+# View current context
+pnpm paperclipai context show
+
+# List profiles
+pnpm paperclipai context list
+
+# Switch profile
+pnpm paperclipai context use default
+```
+
+To avoid storing secrets in context, use an env var:
+
+```sh
+pnpm paperclipai context set --api-key-env-var-name PAPERCLIP_API_KEY
+export PAPERCLIP_API_KEY=...
+```
+
+Context is stored at `~/.paperclip/context.json`.
+
+## Command Categories
+
+The CLI has two categories:
+
+1. **[Setup commands](/cli/setup-commands)** — instance bootstrap, diagnostics, configuration
+2. **[Control-plane commands](/cli/control-plane-commands)** — issues, agents, approvals, activity