Fix bd init --quiet and clarify agent usage in docs

- Fix: bd init --quiet now skips interactive prompts and auto-installs hooks
- Docs: Add Git Workflow & Auto-Sync section to README
- Docs: Update AGENTS.md with --quiet flag guidance for agents
- Docs: Update WORKFLOW.md to explain auto-import after git pull
- Docs: Add FAQ entries about auto-sync behavior and who runs init
- Closes bd-127, bd-140, bd-141

Amp-Thread-ID: https://ampcode.com/threads/T-72f55d41-f16c-4541-b72a-8acc9013e87b
Co-authored-by: Amp <amp@ampcode.com>

AGENTS.md

@@ -4,6 +4,23 @@
 
 This is **beads** (command: `bd`), an issue tracker designed for AI-supervised coding workflows. We dogfood our own tool!
 
+## Human Setup vs Agent Usage
+
+**IMPORTANT:** If you need to initialize bd, use the `--quiet` flag:
+
+```bash
+bd init --quiet  # Non-interactive, auto-installs git hooks, no prompts
+```
+
+**Why `--quiet`?** Regular `bd init` has interactive prompts (git hooks) that confuse agents. The `--quiet` flag makes it fully non-interactive:
+- Automatically installs git hooks
+- No prompts for user input
+- Safe for agent-driven repo setup
+
+**If the human already initialized:** Just use bd normally with `bd create`, `bd ready`, `bd update`, `bd close`, etc.
+
+**If you see "database not found":** Run `bd init --quiet` yourself, or ask the human to run `bd init`.
+
 ## Issue Tracking
 
 We use bd (beads) for issue tracking instead of Markdown TODOs or external tools.