docs: reorganize documentation into concepts, design, and examples
Move documentation files into a clearer structure: - concepts/: core ideas (convoy, identity, molecules, polecat-lifecycle, propulsion) - design/: architecture and protocols (architecture, escalation, federation, mail, etc.) - examples/: demos and tutorials (hanoi-demo) - overview.md: renamed from understanding-gas-town.md Remove outdated/superseded docs and update reference.md. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Steve Yegge
Steve Yegge
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docs/concepts/molecules.md
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206
docs/concepts/molecules.md
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# Molecules
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Molecules are workflow templates that coordinate multi-step work in Gas Town.
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## Molecule Lifecycle
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```
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Formula (source TOML) ─── "Ice-9"
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│
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▼ bd cook
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Protomolecule (frozen template) ─── Solid
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│
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├─▶ bd mol pour ──▶ Mol (persistent) ─── Liquid ──▶ bd squash ──▶ Digest
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│
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└─▶ bd mol wisp ──▶ Wisp (ephemeral) ─── Vapor ──┬▶ bd squash ──▶ Digest
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└▶ bd burn ──▶ (gone)
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```
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## Core Concepts
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| Term | Description |
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|------|-------------|
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| **Formula** | Source TOML template defining workflow steps |
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| **Protomolecule** | Frozen template ready for instantiation |
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| **Molecule** | Active workflow instance with trackable steps |
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| **Wisp** | Ephemeral molecule for patrol cycles (never synced) |
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| **Digest** | Squashed summary of completed molecule |
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## Common Mistake: Reading Formulas Directly
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**WRONG:**
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```bash
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# Reading a formula file and manually creating beads for each step
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cat .beads/formulas/mol-polecat-work.formula.toml
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bd create --title "Step 1: Load context" --type task
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bd create --title "Step 2: Branch setup" --type task
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# ... creating beads from formula prose
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```
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**RIGHT:**
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```bash
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# Cook the formula into a proto, pour into a molecule
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bd cook mol-polecat-work
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bd mol pour mol-polecat-work --var issue=gt-xyz
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# Now work through the step beads that were created
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bd ready # Find next step
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bd close <step-id> # Complete it
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```
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**Key insight:** Formulas are source templates (like source code). You never read
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them directly during work. The `cook` → `pour` pipeline creates step beads for you.
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Your molecule already has steps - use `bd ready` to find them.
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## Navigating Molecules
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Molecules help you track where you are in multi-step workflows.
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### Finding Your Place
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```bash
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bd mol current # Where am I?
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bd mol current gt-abc # Status of specific molecule
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```
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Output:
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```
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You're working on molecule gt-abc (Feature X)
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✓ gt-abc.1: Design
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✓ gt-abc.2: Scaffold
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✓ gt-abc.3: Implement
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→ gt-abc.4: Write tests [in_progress] <- YOU ARE HERE
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○ gt-abc.5: Documentation
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○ gt-abc.6: Exit decision
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Progress: 3/6 steps complete
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```
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### Seamless Transitions
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Close a step and advance in one command:
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```bash
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bd close gt-abc.3 --continue # Close and advance to next step
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bd close gt-abc.3 --no-auto # Close but don't auto-claim next
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```
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**The old way (3 commands):**
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```bash
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bd close gt-abc.3
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bd ready --parent=gt-abc
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bd update gt-abc.4 --status=in_progress
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```
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**The new way (1 command):**
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```bash
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bd close gt-abc.3 --continue
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```
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### Transition Output
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```
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✓ Closed gt-abc.3: Implement feature
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Next ready in molecule:
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gt-abc.4: Write tests
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→ Marked in_progress (use --no-auto to skip)
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```
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### When Molecule Completes
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```
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✓ Closed gt-abc.6: Exit decision
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Molecule gt-abc complete! All steps closed.
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Consider: bd mol squash gt-abc --summary '...'
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```
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## Molecule Commands
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### Beads Operations (bd)
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```bash
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# Formulas
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bd formula list # Available formulas
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bd formula show <name> # Formula details
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bd cook <formula> # Formula → Proto
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# Molecules (data operations)
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bd mol list # Available protos
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bd mol show <id> # Proto details
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bd mol pour <proto> # Create mol
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bd mol wisp <proto> # Create wisp
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bd mol bond <proto> <parent> # Attach to existing mol
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bd mol squash <id> # Condense to digest
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bd mol burn <id> # Discard wisp
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bd mol current # Where am I in the current molecule?
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```
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### Agent Operations (gt)
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```bash
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# Hook management
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gt hook # What's on MY hook
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gt mol current # What should I work on next
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gt mol progress <id> # Execution progress of molecule
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gt mol attach <bead> <mol> # Pin molecule to bead
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gt mol detach <bead> # Unpin molecule from bead
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# Agent lifecycle
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gt mol burn # Burn attached molecule
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gt mol squash # Squash attached molecule
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gt mol step done <step> # Complete a molecule step
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```
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## Polecat Workflow
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Polecats receive work via their hook - a pinned molecule attached to an issue.
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They execute molecule steps sequentially, closing each step as they complete it.
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### Molecule Types for Polecats
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| Type | Storage | Use Case |
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|------|---------|----------|
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| **Regular Molecule** | `.beads/` (synced) | Discrete deliverables, audit trail |
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| **Wisp** | `.beads/` (ephemeral) | Patrol cycles, operational loops |
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Polecats typically use **regular molecules** because each assignment has audit value.
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Patrol agents (Witness, Refinery, Deacon) use **wisps** to prevent accumulation.
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### Hook Management
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```bash
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gt hook # What's on MY hook?
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gt mol attach-from-mail <id> # Attach work from mail message
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gt done # Signal completion (syncs, submits to MQ, notifies Witness)
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```
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### Polecat Workflow Summary
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```
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1. Spawn with work on hook
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2. gt hook # What's hooked?
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3. bd mol current # Where am I?
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4. Execute current step
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5. bd close <step> --continue
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6. If more steps: GOTO 3
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7. gt done # Signal completion
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```
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### Wisp vs Molecule Decision
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| Question | Molecule | Wisp |
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|----------|----------|------|
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| Does it need audit trail? | Yes | No |
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| Will it repeat continuously? | No | Yes |
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| Is it discrete deliverable? | Yes | No |
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| Is it operational routine? | No | Yes |
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## Best Practices
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1. **Use `--continue` for propulsion** - Keep momentum by auto-advancing
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2. **Check progress with `bd mol current`** - Know where you are before resuming
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3. **Squash completed molecules** - Create digests for audit trail
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4. **Burn routine wisps** - Don't accumulate ephemeral patrol data
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