From 5da23385c6d0f2c360c3927e0c921e84a7c8da08 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 25 Aug 2025 20:39:49 -0400
Subject: [PATCH 1/2] Add "directories" description for "study" DatasetType and
 add "docs" where was missing

Apparently I have missed this file entirely whenever I was preparing
  https://github.com/bids-standard/bids-specification/pull/1972 (study DatasetType)

and also due to all the duplication we (I) missed that docs was not listed among "root.subdirs"
or not listed at all.

This would provide a fix, but I wonder if we could/should make it so we could avoid duplication
altogether.  As I have argued in #1972 I feel that "study" is the base dataset type and
next ones just add potentially more to them.  So may be we could come up with some more
compact representation here... but not in this PR
---
 src/schema/rules/directories.yaml | 47 ++++++++++++++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
index 3bfea7c26e..0231b61b7c 100644
--- a/src/schema/rules/directories.yaml
+++ b/src/schema/rules/directories.yaml
@@ -1,5 +1,5 @@
 ---
-# This file defines layouts of directories.
+# This file defines layouts of directories for each DatasetType
 #
 # A layout defines a collection of directory specifiers.
 # Each specifier has a naming convention, requirement level, opacity, and subdirectories.
@@ -16,10 +16,50 @@
 # The special "root" specifier describes the root of the dataset and only defines subdirectories.
 # No naming convention applies, and the requirement level and opacity would be superfluous.
 #
+study:
+  root:
+    subdirs:
+      - code
+      - docs
+      - derivatives
+      - logs
+      - phenotype
+      - sourcedata
+      - stimuli
+  code:
+    name: code
+    level: optional
+    opaque: true
+  docs:
+    name: docs
+    level: optional
+    opaque: true
+  derivatives:
+    name: derivatives
+    level: optional
+    opaque: true
+  logs:
+    name: logs
+    level: optional
+    opaque: true
+  phenotype:
+    name: phenotype
+    level: optional
+    opaque: false
+  sourcedata:
+    name: sourcedata
+    level: optional
+    opaque: true
+  stimuli:
+    name: stimuli
+    level: optional
+    opaque: true
+
 raw:
   root:
     subdirs:
       - code
+      - docs
       - derivatives
       - logs
       - phenotype
@@ -77,6 +117,7 @@ derivative:
   root:
     subdirs:
       - code
+      - docs
       - derivatives
       - logs
       - phenotype
@@ -87,6 +128,10 @@ derivative:
     name: code
     level: optional
     opaque: true
+  docs:
+    name: docs
+    level: optional
+    opaque: true
   derivatives:
     name: derivatives
     level: optional

From e07c730ff2b8815d9c1bc13077d4a4d2db77cbd6 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 26 Aug 2025 09:39:29 -0400
Subject: [PATCH 2/2] Remove "phentoype/" and "stimuli/" from the "root" of the
 "study" dataset

Since per se they should either be under "sourcedata/" or "derivatives/" one way or
another even if it is some stimuli-only dataset(s)
---
 src/schema/rules/directories.yaml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
index 0231b61b7c..e5415e8c14 100644
--- a/src/schema/rules/directories.yaml
+++ b/src/schema/rules/directories.yaml
@@ -23,9 +23,7 @@ study:
       - docs
       - derivatives
       - logs
-      - phenotype
       - sourcedata
-      - stimuli
   code:
     name: code
     level: optional
@@ -42,18 +40,10 @@ study:
     name: logs
     level: optional
     opaque: true
-  phenotype:
-    name: phenotype
-    level: optional
-    opaque: false
   sourcedata:
     name: sourcedata
     level: optional
     opaque: true
-  stimuli:
-    name: stimuli
-    level: optional
-    opaque: true
 
 raw:
   root: