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/recovery/circular-dependencies.md

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+---
+sidebar_position: 4
+title: Circular Dependencies
+description: Detect and break dependency cycles
+---
+
+# Circular Dependencies Recovery
+
+This runbook helps you detect and break circular dependency cycles in your issues.
+
+## Symptoms
+
+- "circular dependency detected" errors
+- `bd blocked` shows unexpected results
+- Issues that should be ready appear blocked
+
+## Diagnosis
+
+```bash
+# Check for blocked issues
+bd blocked
+
+# View dependencies for a specific issue
+bd show <issue-id>
+
+# List all dependencies
+bd dep tree
+```
+
+## Solution
+
+**Step 1:** Identify the cycle
+```bash
+bd blocked --verbose
+```
+
+**Step 2:** Map the dependency chain
+```bash
+bd show <issue-a>
+bd show <issue-b>
+# Follow the chain until you return to <issue-a>
+```
+
+**Step 3:** Determine which dependency to remove
+Consider: Which dependency is least critical to the workflow?
+
+**Step 4:** Remove the problematic dependency
+```bash
+bd dep remove <dependent-issue> <blocking-issue>
+```
+
+**Step 5:** Verify the cycle is broken
+```bash
+bd blocked
+bd ready
+```
+
+## Prevention
+
+- Think "X needs Y" not "X before Y" when adding dependencies
+- Use `bd blocked` after adding dependencies to check for cycles
+- Keep dependency chains shallow when possible

website/docs/recovery/database-corruption.md

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+---
+sidebar_position: 2
+title: Database Corruption
+description: Recover from SQLite database corruption
+---
+
+# Database Corruption Recovery
+
+This runbook helps you recover from SQLite database corruption in Beads.
+
+## Symptoms
+
+- SQLite error messages during `bd` commands
+- "database is locked" errors that persist
+- Missing issues that should exist
+- Inconsistent state between JSONL and database
+
+## Diagnosis
+
+```bash
+# Check database integrity
+bd status
+
+# Look for corruption indicators
+ls -la .beads/beads.db*
+```
+
+If you see `-wal` or `-shm` files alongside `beads.db`, a transaction may have been interrupted.
+
+## Solution
+
+:::warning
+Back up your `.beads/` directory before proceeding.
+:::
+
+**Step 1:** Stop the daemon
+```bash
+bd daemon stop
+```
+
+**Step 2:** Back up current state
+```bash
+cp -r .beads .beads.backup
+```
+
+**Step 3:** Rebuild from JSONL (source of truth)
+```bash
+bd doctor --fix
+```
+
+**Step 4:** Verify recovery
+```bash
+bd status
+bd list
+```
+
+**Step 5:** Restart daemon
+```bash
+bd daemon start
+```
+
+## Prevention
+
+- Avoid interrupting `bd sync` operations
+- Let the daemon handle synchronization
+- Use `bd daemon stop` before system shutdown

website/docs/recovery/index.md

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+---
+sidebar_position: 1
+title: Recovery Overview
+description: Diagnose and resolve common Beads issues
+---
+
+# Recovery Overview
+
+This section provides step-by-step recovery procedures for common Beads issues. Each runbook follows a consistent format: Symptoms, Diagnosis, Solution (5 steps max), and Prevention.
+
+## Common Issues
+
+| Issue | Symptoms | Runbook |
+|-------|----------|---------|
+| Database Corruption | SQLite errors, missing data | [Database Corruption](/recovery/database-corruption) |
+| Merge Conflicts | JSONL conflicts during sync | [Merge Conflicts](/recovery/merge-conflicts) |
+| Circular Dependencies | Cycle detection errors | [Circular Dependencies](/recovery/circular-dependencies) |
+| Sync Failures | `bd sync` errors | [Sync Failures](/recovery/sync-failures) |
+
+## Quick Diagnostic
+
+Before diving into specific runbooks, try these quick checks:
+
+```bash
+# Check Beads status
+bd status
+
+# Verify daemon is running
+bd daemon status
+
+# Check for blocked issues
+bd blocked
+```
+
+:::tip
+Most issues can be diagnosed with `bd status`. Start there before following specific runbooks.
+:::
+
+## Getting Help
+
+If these runbooks don't resolve your issue:
+
+1. Check the [FAQ](/reference/faq)
+2. Search [existing issues](https://github.com/steveyegge/beads/issues)
+3. Open a new issue with diagnostic output

website/docs/recovery/merge-conflicts.md

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+---
+sidebar_position: 3
+title: Merge Conflicts
+description: Resolve JSONL merge conflicts
+---
+
+# Merge Conflicts Recovery
+
+This runbook helps you resolve JSONL merge conflicts that occur during Git operations.
+
+## Symptoms
+
+- Git merge conflicts in `.beads/*.jsonl` files
+- `bd sync` fails with conflict errors
+- Different issue states between clones
+
+## Diagnosis
+
+```bash
+# Check for conflicted files
+git status
+
+# Look for conflict markers
+grep -l "<<<<<<" .beads/*.jsonl
+```
+
+## Solution
+
+:::warning
+JSONL files are append-only logs. Manual editing requires care.
+:::
+
+**Step 1:** Identify conflicted files
+```bash
+git diff --name-only --diff-filter=U
+```
+
+**Step 2:** For each conflicted JSONL file, keep both versions
+```bash
+# Accept both changes (append-only is safe)
+git checkout --ours .beads/issues.jsonl
+git add .beads/issues.jsonl
+```
+
+**Step 3:** Force rebuild to reconcile
+```bash
+bd doctor --fix
+```
+
+**Step 4:** Verify state
+```bash
+bd list
+bd status
+```
+
+**Step 5:** Complete the merge
+```bash
+git commit -m "Resolved beads merge conflicts"
+```
+
+## Prevention
+
+- Sync before and after Git operations
+- Use `bd sync` regularly
+- Avoid concurrent modifications from multiple clones

website/docs/recovery/sync-failures.md

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+---
+sidebar_position: 5
+title: Sync Failures
+description: Recover from bd sync failures
+---
+
+# Sync Failures Recovery
+
+This runbook helps you recover from `bd sync` failures.
+
+## Symptoms
+
+- `bd sync` hangs or times out
+- Network-related error messages
+- "failed to push" or "failed to pull" errors
+- Daemon not responding
+
+## Diagnosis
+
+```bash
+# Check daemon status
+bd daemon status
+
+# Check sync state
+bd status
+
+# View daemon logs
+cat .beads/daemon.log | tail -50
+```
+
+## Solution
+
+**Step 1:** Stop the daemon
+```bash
+bd daemon stop
+```
+
+**Step 2:** Check for lock files
+```bash
+ls -la .beads/*.lock
+# Remove stale locks if daemon is definitely stopped
+rm -f .beads/*.lock
+```
+
+**Step 3:** Force a fresh sync
+```bash
+bd doctor --fix
+```
+
+**Step 4:** Restart daemon
+```bash
+bd daemon start
+```
+
+**Step 5:** Verify sync works
+```bash
+bd sync
+bd status
+```
+
+## Common Causes
+
+| Cause | Solution |
+|-------|----------|
+| Network timeout | Retry with better connection |
+| Stale lock file | Remove lock after stopping daemon |
+| Corrupted state | Use `bd doctor --fix` |
+| Git conflicts | See [Merge Conflicts](/recovery/merge-conflicts) |
+
+## Prevention
+
+- Ensure stable network before sync
+- Let sync complete before closing terminal
+- Use `bd daemon stop` before system shutdown