feat: add llms.txt standard support for AI agent discoverability (#784)

Cherry-picked website/, scripts/generate-llms-full.sh, and deploy-docs.yml
from joyshmitz's PR. Fixed workflow to trigger on main branch instead of
docs/docusaurus-site.

Features:
- Docusaurus documentation site with llms.txt support
- Environment-variable driven config (defaults to steveyegge org)
- Automated llms-full.txt generation from docs
- GitHub Pages deployment workflow

Co-authored-by: joyshmitz <joyshmitz@users.noreply.github.com>

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Executed-By: beads/crew/dave
Rig: beads
Role: crew

website/docs/reference/advanced.md

@@ -0,0 +1,176 @@
+---
+id: advanced
+title: Advanced Features
+sidebar_position: 3
+---
+
+# Advanced Features
+
+Advanced beads functionality.
+
+## Issue Rename
+
+Rename issues while preserving references:
+
+```bash
+bd rename bd-42 bd-new-id
+bd rename bd-42 bd-new-id --dry-run  # Preview
+```
+
+Updates:
+- All dependencies pointing to old ID
+- All references in other issues
+- Comments and descriptions
+
+## Issue Merge
+
+Merge duplicate issues:
+
+```bash
+bd merge bd-42 bd-43 --into bd-41
+bd merge bd-42 bd-43 --into bd-41 --dry-run
+```
+
+What gets merged:
+- Dependencies → target
+- Text references updated across all issues
+- Source issues closed with merge reason
+
+## Database Compaction
+
+Reduce database size by compacting old issues:
+
+```bash
+# View compaction statistics
+bd admin compact --stats
+
+# Preview candidates (30+ days closed)
+bd admin compact --analyze --json
+
+# Apply agent-generated summary
+bd admin compact --apply --id bd-42 --summary summary.txt
+
+# Immediate deletion (CAUTION!)
+bd admin cleanup --force
+```
+
+**When to compact:**
+- Database > 10MB with old closed issues
+- After major milestones
+- Before archiving project phase
+
+## Restore from History
+
+View deleted or compacted issues from git:
+
+```bash
+bd restore bd-42 --show
+bd restore bd-42 --to-file issue.json
+```
+
+## Database Inspection
+
+```bash
+# Schema info
+bd info --schema --json
+
+# Raw database query (advanced)
+sqlite3 .beads/beads.db "SELECT * FROM issues LIMIT 5"
+```
+
+## Custom Tables
+
+Extend the database with custom tables:
+
+```go
+// In Go code using beads as library
+storage.UnderlyingDB().Exec(`
+  CREATE TABLE IF NOT EXISTS custom_table (...)
+`)
+```
+
+See [EXTENDING.md](https://github.com/steveyegge/beads/blob/main/docs/EXTENDING.md).
+
+## Event System
+
+Subscribe to beads events:
+
+```bash
+# View recent events
+bd events list --since 1h
+
+# Watch events in real-time
+bd events watch
+```
+
+Events:
+- `issue.created`
+- `issue.updated`
+- `issue.closed`
+- `dependency.added`
+- `sync.completed`
+
+## Batch Operations
+
+### Create Multiple
+
+```bash
+cat issues.jsonl | bd import -i -
+```
+
+### Update Multiple
+
+```bash
+bd list --status open --priority 4 --json | \
+  jq -r '.[].id' | \
+  xargs -I {} bd update {} --priority 3
+```
+
+### Close Multiple
+
+```bash
+bd list --label "sprint-1" --status open --json | \
+  jq -r '.[].id' | \
+  xargs -I {} bd close {} --reason "Sprint complete"
+```
+
+## API Access
+
+Use beads as a Go library:
+
+```go
+import "github.com/steveyegge/beads/internal/storage"
+
+db, _ := storage.NewSQLite(".beads/beads.db")
+issues, _ := db.ListIssues(storage.ListOptions{
+    Status: "open",
+})
+```
+
+## Performance Tuning
+
+### Large Databases
+
+```bash
+# Enable WAL mode
+bd config set database.wal_mode true
+
+# Increase cache
+bd config set database.cache_size 10000
+```
+
+### Many Concurrent Agents
+
+```bash
+# Use event-driven daemon
+export BEADS_DAEMON_MODE=events
+bd daemons killall
+```
+
+### CI/CD Optimization
+
+```bash
+# Disable daemon in CI
+export BEADS_NO_DAEMON=true
+bd --no-daemon list
+```