From a2a19f2bd54453aace5ef4127a42fd5bca8019c2 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 4 Dec 2025 12:13:59 -0500
Subject: [PATCH 1/3] rf: Split sidecar file determination into separate
 function

---
 src/validators/internal/unusedFile.ts | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/src/validators/internal/unusedFile.ts b/src/validators/internal/unusedFile.ts
index 08dfe77b9..388b6818e 100644
--- a/src/validators/internal/unusedFile.ts
+++ b/src/validators/internal/unusedFile.ts
@@ -35,15 +35,25 @@ export async function unusedStimulus(
 
 const standalone_json = ['dataset_description.json', 'genetic_info.json']
 
+function isSidecarFile(file: BIDSFile): boolean {
+  if (!file.name.endsWith('.json')) {
+    return false
+  }
+  if (standalone_json.includes(file.name)) {
+    return false
+  }
+  // coordsystem.json files are kind-of sidecars, and they're picked up by
+  // associations. We may want to exclude them in the future.
+  return true
+}
+
 export async function sidecarWithoutDatafile(
   schema: GenericSchema,
   dsContext: BIDSContextDataset,
 ) {
-  const unusedSidecars = [...walkFileTree(dsContext.tree, dsContext)].filter(
-    (file) => (!file.viewed && file.name.endsWith('.json') &&
-      !standalone_json.includes(file.name)),
-  )
-  unusedSidecars.forEach((sidecar) => {
-    dsContext.issues.add({ code: 'SIDECAR_WITHOUT_DATAFILE', location: sidecar.path })
-  })
+  for (const file of walkFileTree(dsContext.tree, dsContext)) {
+    if (!file.viewed && isSidecarFile(file)) {
+      dsContext.issues.add({ code: 'SIDECAR_WITHOUT_DATAFILE', location: file.path })
+    }
+  }
 }

From 66e9d647349f9d9bf36300b9d820d5f6f64df3c6 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 4 Dec 2025 12:14:26 -0500
Subject: [PATCH 2/3] feat: Exclude prov files from consideration as sidecars

---
 src/validators/internal/unusedFile.ts | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/validators/internal/unusedFile.ts b/src/validators/internal/unusedFile.ts
index 388b6818e..ef4e117aa 100644
--- a/src/validators/internal/unusedFile.ts
+++ b/src/validators/internal/unusedFile.ts
@@ -42,6 +42,10 @@ function isSidecarFile(file: BIDSFile): boolean {
   if (standalone_json.includes(file.name)) {
     return false
   }
+  // prov files are not sidecars
+  if (file.path.startsWith('/prov/')) {
+    return false
+  }
   // coordsystem.json files are kind-of sidecars, and they're picked up by
   // associations. We may want to exclude them in the future.
   return true

From 3137fa9beffe10696e6f7dc643d07fc6e8a9df1e Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 4 Dec 2025 12:20:40 -0500
Subject: [PATCH 3/3] doc: Changelog entry

---
 changelog.d/20251204_121918_markiewicz_bep028.md | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 changelog.d/20251204_121918_markiewicz_bep028.md

diff --git a/changelog.d/20251204_121918_markiewicz_bep028.md b/changelog.d/20251204_121918_markiewicz_bep028.md
new file mode 100644
index 000000000..0cf378aed
--- /dev/null
+++ b/changelog.d/20251204_121918_markiewicz_bep028.md
@@ -0,0 +1,11 @@
+<!--
+A new scriv changelog fragment.
+
+Uncomment the section that is right (remove the HTML comment wrapper).
+For top level release notes, leave all the headers commented out.
+-->
+
+### Added
+
+- Support for JSON files in `/prov/` as standalone files. Avoiding
+  false positive `SIDECAR_WITHOUT_DATAFILE` errors.