Project Layout

project-layout

Propose and hold a canonical folder layout for a computational-science repository, and keep a single layout document that says what every directory is for. The layout is a contract: every artifact has exactly one home, bulk artifacts never enter version control, and AI-session planning files never mix with project deliverables.

When to use

• Scaffolding a new research repository.
• Answering "where does this go?" for any new file.
• Auditing an existing repo whose layout document has drifted from reality.

When NOT to use

• Mid-project wholesale reorganization without an explicit decision-log entry — moving directories breaks links, history, and muscle memory; propose, record the decision, then move.
• Adding one module to an existing, documented layout — just follow the map; do not re-derive it.
• Deciding project phase status — the layout document must never carry "current phase" information (see Rules).

The canonical shape

Adapt names to the project; keep the separations. The copyable version lives in the pack's templates/project-layout.md.

<project>/
├── README.md                 # summary, install, how to run
├── TODO.md                   # current-iteration execution buffer (ephemeral, rewritten per phase)
├── CLAUDE.md                 # operating rules + the Aletheia config block
├── <env manifest + lockfile> # pyproject.toml + lock, environment.yml, etc. (see run-provenance)
├── docs/
│   ├── README.md             # authority map: which document is current / stale / archived
│   ├── decisions.md          # ADR-lite decision chain (see decision-log)
│   ├── <spec>.md             # implementation spec — the contract code is tested against
│   ├── design/               # full technical design ("why" documents)
│   ├── roadmap/              # long-horizon plan + phase/gate registry
│   ├── build_log/            # write-once phase/gate evidence entries (see build-log)
│   └── archive/              # retired documents — moved, never deleted
├── src/<package>/            # installable package (src-layout)
│   ├── common/               # shared library — imports nothing above it
│   └── <domain subpackages>  # model / analysis / orchestration layers
├── configs/                  # declarative run configurations (reviewer can re-run from these)
├── scripts/                  # reusable CLI pipelines (run repeatedly, produce artifacts)
├── notebooks/                # numbered exploratory narratives + README manifest
├── tests/                    # unit + integration; includes the named correctness gate
├── data/                     # inputs — gitignored, README tracked (see run-provenance)
├── models/                   # trained/fitted artifacts — gitignored
└── results/                  # run evidence — gitignored, selected summaries force-added
                              # (see evidence-convention)

Runbook

1. New repo: copy templates/project-layout.md into docs/, prune directories the project will not use, and create the tree. Create data/README.md, results/README.md stating the gitignore-plus-tracked-README policy before the first run lands.
2. Placement question: read the layout document, place the file, and if the answer was not derivable from the document, add the missing one-line intent to it in the same change.
3. Layout audit: diff the real tree (find . -maxdepth 2 -type d) against the layout document; report undocumented directories and documented-but-absent ones.
4. Record any structural change as a decision-log entry before moving files.

Rules

1. One home per artifact class. Exploratory one-offs → notebooks/; reusable pipelines → scripts/; shared logic → src/<package>/common/; orchestration imports downward, never sideways or up.
2. Import direction is bottom-up. common/ imports nothing from higher layers; orchestration layers import everything below. A violated import direction is a layout bug.
3. Bulk directories are gitignored, their READMEs are tracked. data/, models/, results/ accumulate gigabytes; version the policy and provenance (READMEs, meta files, selected summaries via explicit force-add), not the bulk.
4. The layout document never states current phase or status. Status is derived from git history, the build log, and the roadmap's status board — a status line in a layout file is a drift source by construction.
5. Session artifacts are not deliverables. Plans, task breakdowns, and scratch specs generated during AI-assisted sessions live under .claude/plans/ (or the harness equivalent), never in docs/, scripts/, or the repo root. docs/ holds only artifacts the project's papers and reports derive from.
6. Retired documents move to docs/archive/, never get deleted. Superseded specs remain citable; the docs authority map (docs/README.md) records what is current.
7. Every directory earns a one-line intent in the layout document. A directory nobody can describe in one line is a candidate for removal.

Placement + notebook discipline

Rule 1 states the routing (one-offs → notebooks/, pipelines → scripts/, shared logic → the package); the discipline below is how each destination avoids its characteristic rot — notebooks rot as un-diffable pipelines, scripts rot as unread one-offs, copy-pasted logic rots everywhere at once.

• The notebook is the default; a script is earned by re-run demand, not granted by optimism. Second manual re-run of a notebook for fresh outputs is the promotion signal: move the logic into the package, wrap a CLI script around it, keep the notebook as the narrative importing the same functions, and note the promotion in the manifest.
• Numbered series with a manifest. NN_kebab-topic.ipynb, numbering append-only (reusing a number breaks every citation to the old one); notebooks/README.md states each notebook's role and rerun policy (live / frozen / archived).
• Execute top-to-bottom before commit. A committed notebook carries its outputs — run it in place (e.g. jupyter nbconvert --execute --inplace) so the repo version shows what the code actually produces. A stale committed notebook is a bug: re-execute it or mark it frozen/archived. Retired series move to notebooks/archive/, numbers never reused (historical notebooks pinned to old APIs are narrative, not drift — layer-sync rule 7).
• Narrative is the point; no library logic in cells. Prose cells state the question, method, and reading of each figure — a notebook that is only code should have been a script, and the moment a function is worth reusing it moves to the package. Scripts orchestrate (argument parsing + calls into src/ + output writing); heavy logic inside a script is library code in hiding. Never edit defaults to probe — a probe is a notebook cell or a script flag (canonical-params).

Configuration

Reads from the Aletheia config block in the adopter's CLAUDE.md:

• {{evidence_dir}} — the run-evidence root (default results/).
• {{decision_log}} — the decision chain file (default docs/decisions.md).
• {{build_log_dir}} — the build-log directory (default docs/build_log/).

Provenance & maintenance

Generalized from the working layout of a mature computational-research repository (src-layout package, shared-library import discipline, gitignored bulk dirs with tracked READMEs, docs authority map, session-artifact separation); see the pack's examples/ directory for the worked exemplar mapping. The tree above is a verified pattern; directory names are adaptable, the separations are the invariant. Inference is labeled where it occurs.

Re-verify in your project:

• git check-ignore data results models — confirms bulk directories are ignored (paths that print are ignored; adjust to your names).
• test -f docs/README.md && test -f {{decision_log}} — confirms the authority map and decision chain exist.
• find . -maxdepth 2 -type d -not -path './.git*' — diff this against the layout document for undocumented directories.