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title: Monorepo Decomposition Plan tags: [plan, architecture, infrastructure, monorepo] created: 2026-05-20 updated: 2026-05-27 status: active related:

• “decouple-backend-plan”
• “platform”

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Monorepo Decomposition Plan

Objective

Dissolve the monorepo (lemna-dev) into fully independent floating repositories. Zero submodules. Zero super-repos. Each repo is sovereign.

Repos After Decomposition (34 total, 0 submodules)

New repos (3)

Repo	Contains	Origin
lemna-knowledge	knowledge/ (cookbook, inventory, journal, templates)	monorepo root
lemna-opencode	.opencode/ (skills, commands, tools, opencode.json) + AGENTS.md	monorepo root
data-scraping	data-scraping/ (plans, sources, paper_collection.json)	monorepo root

Freed existing repos (31)

Repo	Current submodule path
kitchenware	src/kitchenware
pantry	src/pantry
lemna-sdk	pipeline/backend/lemna-sdk
database	pipeline/backend/database
secrets	pipeline/backend/secrets
bucket	pipeline/backend/bucket
pesto	models/pesto
pesto-screen	models/pesto-screen
pomodoro	models/pomodoro
oracle	models/oracle
backmap	models/backmap
carbonara	models/carbonara
carbonara-binders	models/carbonara-binders
carbonara-clip	models/carbonara-clip
novodish	models/novodish
structures	datasets/structures
binders	datasets/binders
endpoint-pesto	pipeline/services/endpoint-pesto
endpoint-pesto-screen	pipeline/services/endpoint-pesto-screen
endpoint-carbonara	pipeline/services/endpoint-carbonara
endpoint-carbonara-binders	pipeline/services/endpoint-carbonara-binders
endpoint-boltz	pipeline/services/endpoint-boltz
endpoint-boltzgen	pipeline/services/endpoint-boltzgen
endpoint-cpmp	pipeline/services/endpoint-cpmp
endpoint-openmm	pipeline/services/endpoint-openmm
endpoint-rfdiffusion	pipeline/services/endpoint-rfdiffusion
workflow-binder-design	pipeline/workflows/binder-design
workflow-debug	pipeline/workflows/debug
workspace-backmap	pipeline/workspace/backmap
workspace-binders-design-pipeline	pipeline/workspace/binders-design-pipeline
project-pesto	pipeline/projects/pesto
project-carbonara	pipeline/projects/carbonara
website	website/website
molstar-bfactor	website/packages/molstar-bfactor
dashboard	tools/dashboard
molstar-viewer	tools/molstar-viewer

File Disposition

Move to new repos

File/directory	Destination
knowledge/ (entire directory)	lemna-knowledge/
.opencode/ (entire directory)	lemna-opencode/
AGENTS.md	lemna-opencode/AGENTS.md
data-scraping/ (entire directory)	data-scraping/

Fold into knowledge (historical docs)

File/directory	Destination
pipeline/backend/refactor/MIGRATION-PLAN.md	lemna-knowledge/journal/sessions/done/
pipeline/backend/refactor/recover_pssm.sh	lemna-knowledge/journal/sessions/done/
pipeline/PLAN-decouple-backend.md	lemna-knowledge/journal/sessions/done/

Resolved

File/directory	Decision
pipeline/backend/tests/	Deleted — SDK integration tests overlap with lemna-sdk’s own tests; endpoint tests are in each endpoint repo

Move into existing repos

File	Destination	Note
export.json	pantry/ repo config	Pantry owns namespace resolution; update pantry code to self-resolve
scripts/pty-push-all.sh	pantry/scripts/	If still used; otherwise delete

Split and redistribute

File (root justfile)	Destination	Commands
sync / format / check / test	kitchenware/justfile	Already has its own; merge root versions in
marimo util	Repo that uses it (e.g. novodish)
tensorboard util	Model repos that use it
molstar util	molstar-viewer repo

Delete

File/directory	Reason
.hermes/	Not needed
pipeline/backend/docker-compose.yml	Super compose being removed
pipeline/backend/Caddyfile	Part of super compose
scripts/git-all.sh	Walked submodules; no submodules exist
scripts/apply-all.sh	Same
.gitmodules	No monorepo
.gitignore (root)	Each repo owns its own

Already independent — just remove the pointer

All 36 .gitmodules entries. Each is already its own repo with its own git history. The monorepo only tracked which commit they sat on.

What You Lose and Replacements

Capability	Replacement
lazygit across all repos	Per-repo lazygit. Or alias to open lazygit in 2-3 active repos
git-all cross-repo git commands	Gone. Push per-repo
apply-all batch endpoint commands	Each endpoint repo runs its own justfile
Submodule commit sync	Pin deps in pyproject.toml via git URLs + tags
Single .gitignore / conventions	Each repo owns its own (mostly already do)
Super docker-compose for backend	Each backend service runs its own compose independently

Dependency Updates

Replace workspace path dependencies in pyproject.toml with git URLs:

# Before
kitchenware = { path = "../../src/kitchenware" }
 
# After
kitchenware = { git = "https://github.com/lemnabio/kitchenware", tag = "v0.4.1" }

Notable files to update:

• Any endpoint pyproject.toml referencing kitchenware or SDK via path

Pantry Namespace Resolution (design needed)

Currently export.json maps namespace names to monorepo paths:

{
  "pesto": "models/pesto",
  "carbonara": "models/carbonara",
  ...
}

Options for replacement:

1. Local config (~/.config/lemna/namespaces.toml) — maps namespace → repo URL or local path
2. Self-declaration — each repo has a .pantry.toml declaring its namespace; pantry discovers siblings
3. Remote resolution — pantry queries GitHub org to find repos by convention

Not a blocker for decomposition. Can be addressed as a pantry-internal refactor after.

Migration Steps (ordered)

1. Create lemna-knowledge, copy knowledge/ + fold in historical docs, push
2. Create lemna-opencode, copy .opencode/ + AGENTS.md, update skill paths that reference monorepo-relative locations, push
3. Create data-scraping, copy data-scraping/, push
4. Decide destination for pipeline/backend/tests/, move it Resolved: deleted
5. Move export.json into pantry/, update pantry namespace resolution
6. Move pty-push-all.sh into pantry/scripts/ or delete
7. Split root justfile into per-repo justfiles, delete root
8. Delete: .hermes/, super compose files, scripts/, .gitmodules, root .gitignore
9. Update all pyproject.toml path deps to git URLs
10. Tag monorepo as last-monorepo, push, stop using it

Open Questions

• Where does pipeline/backend/tests/ land? Deleted — SDK tests in lemna-sdk, endpoint tests in each endpoint repo
• Pantry namespace resolution design (local config vs self-declaration vs remote)
• Which model repos use the root justfile’s marimo/tensorboard utils? Need per-repo placement