From fb1b002101bf8ddf9e56d8e9c194c85b9467b133 Mon Sep 17 00:00:00 2001
From: Michelle Wang <tomichellewang@gmail.com>
Date: Sat, 16 Aug 2025 11:01:47 -0400
Subject: [PATCH 1/2] add `scratch/` subdirectory to schema (following `docs/`
 PR changes)

---
 src/common-principles.md                | 1 +
 src/schema/rules/directories.yaml       | 4 ++++
 src/schema/rules/files/common/core.yaml | 3 +++
 3 files changed, 8 insertions(+)

diff --git a/src/common-principles.md b/src/common-principles.md
index d15cfa937a..6efa5a262a 100644
--- a/src/common-principles.md
+++ b/src/common-principles.md
@@ -394,6 +394,7 @@ Derivatives can be stored/distributed in two ways:
     MAY be included in the `code/` subdirectory.
     Extra documentation (and relevant images) MAY be included in the `docs/` subdirectory.
     Logs from running the code or other commands MAY be stored under `logs/` subdirectory.
+    Temporary working files MAY be stored under the `scratch/` subdirectory.
 
     Example of a derivative dataset including the raw dataset as source:
 
diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
index 3bfea7c26e..ecfce3af87 100644
--- a/src/schema/rules/directories.yaml
+++ b/src/schema/rules/directories.yaml
@@ -46,6 +46,10 @@ raw:
     name: phenotype
     level: optional
     opaque: false
+  scratch:
+    name: scratch
+    level: optional
+    opaque: true
   sourcedata:
     name: sourcedata
     level: optional
diff --git a/src/schema/rules/files/common/core.yaml b/src/schema/rules/files/common/core.yaml
index fe8535d0ce..897923d7c8 100644
--- a/src/schema/rules/files/common/core.yaml
+++ b/src/schema/rules/files/common/core.yaml
@@ -42,6 +42,9 @@ docs:
 logs:
   level: optional
   path: logs
+scratch:
+  level: optional
+  path: scratch
 sourcedata:
   level: optional
   path: sourcedata

From a9e938b2ac5fd4eb634411e6189d41447814ac65 Mon Sep 17 00:00:00 2001
From: Michelle Wang <tomichellewang@gmail.com>
Date: Tue, 2 Sep 2025 10:34:44 -0400
Subject: [PATCH 2/2] add scratch to "study" and remove from "raw"

---
 src/schema/rules/directories.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
index 5629e6f442..59e728d85b 100644
--- a/src/schema/rules/directories.yaml
+++ b/src/schema/rules/directories.yaml
@@ -23,6 +23,7 @@ study:
       - docs
       - derivatives
       - logs
+      - scratch
       - sourcedata
   code:
     name: code
@@ -40,6 +41,10 @@ study:
     name: logs
     level: optional
     opaque: true
+  scratch:
+    name: scratch
+    level: optional
+    opaque: true
   sourcedata:
     name: sourcedata
     level: optional
@@ -76,10 +81,6 @@ raw:
     name: phenotype
     level: optional
     opaque: false
-  scratch:
-    name: scratch
-    level: optional
-    opaque: true
   sourcedata:
     name: sourcedata
     level: optional