---

name: light-project-structure description: >- Audit, plan, scaffold, and safely migrate research project structures across greenfield, existing Git/non-Git repositories, and monorepo subroots. Use for project folders, repository cleanup, source inventory, move maps, naming and storage policy, Python/R/mixed/LaTeX profiles, template provenance, conflict review, applied-move evidence, or rollback. Existing projects are read-only until the user authorizes exact action IDs bound to a plan digest. Preserve uncommitted and untracked work, symlinks, submodules, and memory-pm's .light content. This is an off-DAG local tool: do not emit findings or invent a STAGE_GATES/ROUTES connection.

Project structure lifecycle

Own the visible project tree and its migration evidence. Do not mistake a tidy directory for reproducible research.

Read references/project-lifecycle-resource-map.md before an existing-repository migration. It defines artifacts, policy, access levels, provenance, and cross-skill ownership. Use references/structure-profiles.json for small profile minima and templates/project-policy.template.json for explicit project/file policy. Use scripts/structure_governance_gate.py before delivery to validate profile choice, existing-project read-only safety, template residuals, secret scan, environment doctor, authorization binding, applied-manifest binding, and rollback evidence.

Non-negotiable boundary

1. Treat inventory as read-only access, not authorization to move.
2. Never overwrite, delete, run git rm --cached, initialize DVC, rewrite configuration, or move a symlink automatically.
3. Never use --force as consent. The lifecycle has no force bypass.
4. Preserve all .light/ content. memory-pm alone creates or edits passport, project card, decision log, version history, terminology, and handoff files.
5. Keep absent facts UNKNOWN. A path such as data/raw does not prove size, sensitivity, immutability, recomputability, or Git policy.
6. Do not turn this overlay into a DAG node. Emit no light.findings.v1; add no STAGE_GATES, ROUTES, stage number, or back-edge.
7. State that structural conformance does not prove data quality, experiment reproducibility, statistical validity, or paper quality.
8. Never ship a generated or migrated tree with unresolved template placeholders, unhandled secret-scan hits, or missing required Python/R/environment checks.

Choose the mode

Situation	Mode
Empty target and the user wants a starting tree	scaffold with one explicit profile
Existing repository, monorepo package, or non-Git directory	intake, then stop at the decision
User approved exact moves after seeing the plan	create authorization, then apply
Applied moves need reversal	rollback from the applied manifest

Do not scaffold a non-empty directory. Do not retrofit a fixed 23-directory tree onto R, paper-only, mixed-language, custom, or monorepo projects.

Phase 1 — Intake and requirements

Collect or preserve as UNKNOWN:

• project type and whether the selected root is a Git root, monorepo subroot, or non-Git directory;
• deliverables, compute environment, data volume, remote storage, collaborators, CI, license, and retention;
• Git root, branch, tracked/untracked/ignored state, uncommitted changes, submodules, symlinks, large files, and sensitive path signals.

Choose the smallest profile after inspecting observed technology signatures and the user's declared deliverables:

• python-research
• r-research
• mixed-research
• paper-only
• existing-custom

Profiles are extensible minima, not compliance verdicts. The selected profile is not evidence about the project. intake records observed file/config signals separately from policy-declared artifact types, recommends a profile, and fails the governance gate when a different profile has no concrete profile_selection_reason.

Copy the policy template outside the source root, fill known project facts, and add file rules only where there is evidence. Legitimate tracked artifacts include small public fixtures, reviewed golden files, DVC pointers, final paper figures, release artifacts, or audit evidence when project policy requires them. Large/sensitive source data, models, and results usually need DVC/object storage, but require a decision rather than a directory-name verdict.

Run:

python scripts/scaffold.py intake <root> --out <evidence-dir> \
  --profile mixed-research --policy <project-policy.json>

The command writes evidence to --out and verifies that the source snapshot and Git status did not change.

intake also emits technology signatures, the environment doctor, template residual scan, secret scan, and governance report named in the resource map. Tool checks derive from observed or explicitly declared artifact types, not from the chosen profile alone. If the project requires Python, R, Quarto, DVC, LaTeX, or other local tools, record those requirements in the policy. Use the standalone doctor command only when you need an extra ad-hoc check:

python scripts/structure_governance_gate.py --doctor python r

Phase 2 — Review the dry-run

Read the intake artifacts named in the resource map. Check:

• every inventory row has locator/hash/size/Git state plus explicit or UNKNOWN owner, producer, recomputability, sensitivity, classification, target, and policy basis;
• technology signatures identify their locator and distinguish observed evidence from policy.project.artifact_types; the selected profile matches the recommendation or has a concrete user override reason;
• duplicates are evidence, never auto-delete instructions;
• symlinks, existing targets, and many-to-one moves are blocked;
• ../, absolute, drive-letter, UNC, or otherwise root-escaping action paths are blocked in the dry-run plan and governance gate, not deferred to apply;
• a monorepo subroot uses paths relative to that subroot without treating the whole Git root as its project;
• .light/ is preserved and has no move action;
• large tracked fixtures are not condemned merely for being under raw;
• large recomputable or sensitive artifacts surface a storage-policy decision.
• template provenance, residual placeholder scan, secret scan, and environment doctor are present when relevant; .env ignore is not a secret-scan result.

Present:

1. the recommended profile and why;
2. safe action IDs;
3. blocked conflicts and unknowns;
4. separate decisions for move/rename, overwrite (not supported), deletion, git rm --cached, configuration rewrite, and DVC initialization;
5. the plan SHA-256.

Then stop. Ask which action IDs the user authorizes. Do not prewrite their answer.

Run the governance gate on the delivery bundle before presenting a structure as ready:

python scripts/structure_governance_gate.py \
  --input templates/project-structure-governance.example.json

The bundled example is intentionally fail-closed: it attempts scaffold on an existing R project, leaves template placeholders, reports secret values, misses R, uses force, moves .light/, duplicates action IDs, applies delete, moves a symlink, and risks overwrite.

Phase 3 — Bind authorization

After the user chooses, create an authorization document:

{
  "schema": "light.project-structure.v2.authorization",
  "authorization_id": "<user-created stable authorization id>",
  "plan_sha256": "<exact migration-plan plan_sha256>",
  "approved_action_ids": ["move-0001"],
  "authorized_by": "<user-supplied identifier>",
  "authorized_at": "<YYYY-MM-DD>"
}

Do not include blocked or unknown actions. authorization_id and authorized_by must be concrete user-supplied values, not template text; authorized_at cannot be in the future. A changed plan requires fresh authorization. The authorization cannot resolve an overwrite or bypass a symlink block.

Phase 4 — Apply, verify, rollback, reapply

python scripts/scaffold.py apply \
  --plan <migration-plan.json> \
  --authorization <authorization.json> \
  --manifest-out <applied-manifest.json> \
  --as-of <YYYY-MM-DD>

python scripts/scaffold.py rollback \
  --manifest <applied-manifest.json> \
  --rollback-out <rollback-manifest.json>

apply re-verifies source hashes and absolute containment, creates missing target parents, refuses existing targets, moves only ordinary files, records before/after SHA-256, and writes an applied manifest that binds the exact plan file and authorization file by locator plus file SHA-256. A path that escaped the selected root should already have been marked blocked during planning; if one reaches apply anyway, apply still fails closed. rollback verifies target hashes and refuses to overwrite a reappeared source; it uses the applied manifest for safe restoration and does not require the original plan/auth files to still be present.

After rollback:

1. compare the source snapshot and Git status with intake;
2. verify untracked drafts and .light/ content remain byte-identical;
3. reapply only if the authorization remains intended;
4. report unresolved conflicts and separate manual Git/DVC decisions.

Greenfield scaffold

Use only on an empty target:

python scripts/scaffold.py scaffold <target> --profile r-research --name <name>

The command records profile and generator hashes in .project-structure-provenance.json. It is one-time generation, not safe template updating. For managed template evolution, evaluate Copier or Cruft and review local modifications and conflicts; do not claim drift detection is a merge guarantee.

Ownership handoff

• Ask memory-pm to run pm.py init when .light/ memory is needed; do not do its work here.
• Hand data quality, lineage, and release design to data-engineering.
• Hand run manifests and executable reproducibility to experiment-coding.
• Let file-reading understand supplied repositories/materials; this skill alone owns moves.
• Let orchestrator consume a delivery if useful; do not create a gate.

Validation

Run the script self-test:

python scripts/scaffold.py --selftest
python scripts/structure_governance_gate.py --selftest

It exercises source-read-only intake, a tracked fixture policy, generated environment/template/secret/governance reports, an untracked draft, .light/ preservation, authorization binding, applied-manifest plan/auth file binding, real move/hash evidence, rollback, reapply, non-Git mode, monorepo subroot handling, profile scaffold idempotence, and a best-effort Windows symlink branch.

Before delivery, verify:

• No source mutation occurred during intake.
• The user saw conflicts, unknowns, action IDs, and plan digest before apply.
• Applied moves exactly match authorized IDs and have before/after hashes.
• Applied manifest binds the exact migration-plan file and authorization file by locator and file SHA-256.
• No target was overwritten and no symlink was moved.
• No planned/applied source or target path escapes the selected project root.
• Untracked work and .light/ content survived move and rollback.
• Fixtures/golden files/DVC pointers were classified by policy, not path.
• Template residual scan, secret scan, environment doctor, and profile reason are present; observed/declared signatures support the profile, and R/Python requirements are checked when claimed.
• structure_governance_gate.py passes for the actual delivery bundle.
• Template source/version/hash/parameters and update limitation are recorded.
• The delivery does not claim that structure proves reproducibility.