docs: add molecular chemistry documentation (bd-ul59)

Create docs/MOLECULES.md with comprehensive coverage of:
- Layer cake architecture (formulas → protos → molecules → epics → issues)
- Phase metaphor (solid/proto, liquid/mol, vapor/wisp)
- Phase transitions (pour, wisp create, squash, burn)
- Bonding patterns (proto+proto, proto+mol, mol+mol)
- Agent pitfalls (temporal language, forgetting to squash)
- Orphan vs stale matrix
- Progress tracking (computed, not stored)
- Parallelism model (default parallel, opt-in sequential)

Update CLI_REFERENCE.md with Molecular Chemistry section covering:
- Proto/template commands
- Pour command
- Wisp commands
- Bonding commands
- Squash and burn commands

Update ARCHITECTURE.md with cross-reference to new MOLECULES.md.

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

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

docs/ARCHITECTURE.md

@@ -269,6 +269,8 @@ open ──▶ in_progress ──▶ closed
 
 **Molecules** are template work items that define structured workflows. When spawned, they create **wisps** - ephemeral child issues that track execution steps.
 
+> **For full documentation** on the molecular chemistry metaphor (protos, pour, bond, squash, burn), see [MOLECULES.md](MOLECULES.md).
+
 ### Wisp Lifecycle
 
 ```
@@ -317,6 +319,7 @@ The `bd mol squash` command uses hard delete intentionally - tombstones would be
 
 ## Related Documentation
 
+- [MOLECULES.md](MOLECULES.md) - Molecular chemistry metaphor (protos, pour, bond, squash, burn)
 - [INTERNALS.md](INTERNALS.md) - FlushManager, Blocked Cache implementation details
 - [DAEMON.md](DAEMON.md) - Daemon management and configuration
 - [EXTENDING.md](EXTENDING.md) - Adding custom tables to SQLite