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/workflows/molecules.md

@@ -0,0 +1,166 @@
+---
+id: molecules
+title: Molecules
+sidebar_position: 2
+---
+
+# Molecules
+
+Molecules are work graphs created from formulas.
+
+## What is a Molecule?
+
+A molecule is a persistent instance of a formula:
+- Contains steps with dependencies
+- Tracked in `.beads/` (syncs with git)
+- Steps map to issues with parent-child relationships
+
+## Creating Molecules
+
+### From Formula
+
+```bash
+# Pour a formula into a molecule
+bd pour <formula-name> [--var key=value]
+```
+
+**Example:**
+```bash
+bd pour release --var version=1.0.0
+```
+
+This creates:
+- Parent issue: `bd-xyz` (the molecule root)
+- Child issues: `bd-xyz.1`, `bd-xyz.2`, etc. (the steps)
+
+### Listing Molecules
+
+```bash
+bd mol list
+bd mol list --json
+```
+
+### Viewing a Molecule
+
+```bash
+bd mol show <molecule-id>
+bd dep tree <molecule-id>  # Shows full hierarchy
+```
+
+## Working with Molecules
+
+### Step Dependencies
+
+Steps have `needs` dependencies:
+
+```toml
+[[steps]]
+id = "implement"
+title = "Implement feature"
+needs = ["design"]  # Must complete design first
+```
+
+The `bd ready` command respects these:
+
+```bash
+bd ready  # Only shows steps with completed dependencies
+```
+
+### Progressing Through Steps
+
+```bash
+# Start a step
+bd update bd-xyz.1 --status in_progress
+
+# Complete a step
+bd close bd-xyz.1 --reason "Done"
+
+# Check what's ready next
+bd ready
+```
+
+### Viewing Progress
+
+```bash
+# See blocked steps
+bd blocked
+
+# See molecule stats
+bd stats
+```
+
+## Molecule Lifecycle
+
+```
+Formula (template)
+    ↓ bd pour
+Molecule (instance)
+    ↓ work steps
+Completed Molecule
+    ↓ optional cleanup
+Archived
+```
+
+## Advanced Features
+
+### Bond Points
+
+Formulas can define bond points for composition:
+
+```toml
+[compose]
+[[compose.bond_points]]
+id = "entry"
+step = "design"
+position = "before"
+```
+
+### Hooks
+
+Execute actions on step completion:
+
+```toml
+[[steps]]
+id = "build"
+title = "Build project"
+
+[steps.on_complete]
+run = "make build"
+```
+
+### Pinning Work
+
+Assign molecules to agents:
+
+```bash
+# Pin to current agent
+bd pin bd-xyz --start
+
+# Check what's pinned
+bd hook
+```
+
+## Example Workflow
+
+```bash
+# 1. Create molecule from formula
+bd pour feature-workflow --var name="dark-mode"
+
+# 2. View structure
+bd dep tree bd-xyz
+
+# 3. Start first step
+bd update bd-xyz.1 --status in_progress
+
+# 4. Complete and progress
+bd close bd-xyz.1
+bd ready  # Shows next steps
+
+# 5. Continue until complete
+```
+
+## See Also
+
+- [Formulas](/workflows/formulas) - Creating templates
+- [Gates](/workflows/gates) - Async coordination
+- [Wisps](/workflows/wisps) - Ephemeral workflows