Steve Yegge 5e971bd90a 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>

2025-12-24 19:31:14 -08:00

..

dev-notes

docs: fix broken relative links across documentation

2025-12-16 00:46:08 -08:00

ADAPTIVE_IDS.md

docs: fix broken relative links across documentation

2025-12-16 00:46:08 -08:00

ADVANCED.md

Merge GH#409

2025-12-16 01:19:07 -08:00

AIDER_INTEGRATION.md

Add Aider integration for beads issue tracking

2025-11-23 15:13:54 -08:00

ANTIVIRUS.md

feat: add Windows code signing infrastructure (bd-14v0)

2025-12-24 00:07:16 -08:00

ARCHITECTURE.md

docs: add molecular chemistry documentation (bd-ul59)

2025-12-24 19:31:14 -08:00

ATTRIBUTION.md

…

CLAUDE_INTEGRATION.md

docs: document bd setup command

2025-12-16 01:08:42 -08:00

CLAUDE.md

docs: fix broken relative links across documentation

2025-12-16 00:46:08 -08:00

CLI_REFERENCE.md

docs: add molecular chemistry documentation (bd-ul59)

2025-12-24 19:31:14 -08:00

COLLISION_MATH.md

docs: fix broken relative links across documentation

2025-12-16 00:46:08 -08:00

CONFIG.md

bd sync: 2025-12-23 23:38:57

2025-12-24 00:06:41 -08:00

DAEMON.md

docs(daemon): update event-driven mode documentation

2025-12-22 18:49:46 -05:00

DELETIONS.md

refactor(mol): remove bd mol spawn - use pour/wisp only (bd-8y9t)

2025-12-24 12:52:47 -08:00

ERROR_HANDLING.md

docs: Complete error handling audit

2025-11-24 00:35:04 -08:00

EXCLUSIVE_LOCK.md

…

EXTENDING.md

docs: fix broken relative links across documentation

2025-12-16 00:46:08 -08:00

FAQ.md

Merge bd-2k5f-pumpjack: GH#483

2025-12-16 01:18:02 -08:00

GIT_INTEGRATION.md

docs: update beads.jsonl references to issues.jsonl

2025-12-16 01:08:46 -08:00

graph-links.md

refactor: remove bd mail commands - mail moves to Gas Town

2025-12-20 17:56:46 -08:00

INSTALLING.md

Merge GH#518 setup docs

2025-12-16 01:18:51 -08:00

INTERNALS.md

bd sync: 2025-11-25 11:35:26

2025-11-25 11:35:26 -08:00

LABELS.md

docs: fix broken relative links across documentation

2025-12-16 00:46:08 -08:00

LINTING.md

Document -short flag, update linting baseline, clarify bd edit MCP exclusion

2025-11-06 19:42:01 -08:00

MOLECULES.md

docs: add molecular chemistry documentation (bd-ul59)

2025-12-24 19:31:14 -08:00

MULTI_REPO_AGENTS.md

docs: update beads.jsonl references to issues.jsonl

2025-12-16 01:08:46 -08:00

MULTI_REPO_HYDRATION.md

Extract SQLite migrations into separate files (bd-fb95094c.7)

2025-11-06 20:06:45 -08:00

MULTI_REPO_MIGRATION.md

Merge GH#409

2025-12-16 01:19:07 -08:00

PERFORMANCE_TESTING.md

docs: add performance testing guide (bd-zj8e)

2025-11-28 23:26:24 -08:00

PLUGIN.md

feat: add Git worktree compatibility (PR #478)

2025-12-13 12:50:33 -08:00

PROTECTED_BRANCHES.md

Merge GH#409

2025-12-16 01:19:07 -08:00

QUICKSTART.md

refactor: Remove legacy MCP Agent Mail integration (bd-6gd)

2025-12-17 23:14:23 -08:00

README_TESTING.md

DOCTOR IMPROVEMENTS: visual improvements/grouping + add comprehensive tests + fix gosec warnings (#656)

2025-12-20 03:10:06 -08:00

RELEASING.md

docs: fix broken relative links across documentation

2025-12-16 00:46:08 -08:00

ROUTING.md

…

SETUP.md

feat: add Factory.ai (Droid) support to bd setup command (#598)

2025-12-16 13:42:43 -08:00

TESTING_PHILOSOPHY.md

DOCTOR IMPROVEMENTS: visual improvements/grouping + add comprehensive tests + fix gosec warnings (#656)

2025-12-20 03:10:06 -08:00

TESTING.md

chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)

2025-12-22 21:30:57 -08:00

TROUBLESHOOTING.md

Merge GH#409

2025-12-16 01:19:07 -08:00

UI_PHILOSOPHY.md

feat(ux): reorganize command groups and add Tufte-inspired help styling

2025-12-20 12:57:16 -08:00

ui-philosophy.md

refactor(ui): standardize on lipgloss semantic color system

2025-12-20 17:09:50 -08:00

UNINSTALLING.md

chore: remove obsolete BD_GUIDE.md references

2025-12-20 20:50:33 -08:00

WORKTREES.md

Merge bd-2k5f-pumpjack: GH#483

2025-12-16 01:18:02 -08:00