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>

WORKFLOW.md

@@ -377,28 +377,39 @@ ls -lh project.db
 
 ## Git Workflow
 
-### Committing the Database
+### Auto-Sync Behavior
 
-**The database IS your project state.** Commit it!
+bd automatically keeps your database and git in sync:
 
+**Making changes:**
 ```bash
-# Add database to git
-git add project.db
+bd create "New task" -p 1
+bd update bd-5 --status in_progress
+# bd automatically exports to .beads/issues.jsonl after 5 seconds
 
-# Commit with meaningful message
-git commit -m "Updated tracker: completed auth (bd-3), ready for API work"
-
-# Push
+git add .beads/issues.jsonl
+git commit -m "Started working on bd-5"
 git push
 ```
 
+**After git pull:**
+```bash
+git pull
+# bd automatically detects JSONL is newer on next command
+
+bd ready  # Auto-imports fresh data from git!
+bd list --status in_progress  # See what you were working on
+```
+
 ### Multi-Machine Workflow
 
 **Machine 1:**
 ```bash
-beads create "New task" -p 1
-beads update bd-5 --status in_progress
-git add project.db
+bd create "New task" -p 1
+bd update bd-5 --status in_progress
+# Wait 5 seconds for auto-export, or run: bd sync
+
+git add .beads/issues.jsonl
 git commit -m "Started working on bd-5"
 git push
 ```
@@ -406,10 +417,18 @@ git push
 **Machine 2:**
 ```bash
 git pull
-beads ready  # Sees bd-5 is in progress
-beads list --status in_progress  # See what you were working on
+bd ready  # Auto-imports, sees bd-5 is in progress
 ```
 
+### Zero-Lag Sync (Optional)
+
+Install git hooks for immediate sync:
+```bash
+cd examples/git-hooks && ./install.sh
+```
+
+This eliminates the 5-second debounce and guarantees import after `git pull`.
+
 ### Team Workflow
 
 **Each developer has their own database:**