feat: Prune derivatives from main file tree

Once broken into separate trees that can be validated, we can save time
and false positives by removing the derivatives directory from the main
validation context.

bids-validator/src/validators/bids.ts

@@ -70,21 +70,27 @@ export async function validate(
     issues.addNonSchemaIssue('MISSING_DATASET_DESCRIPTION', [] as IssueFile[])
   }
 
-  let derivatives: FileTree[] = []
+  const bidsDerivatives: FileTree[] = []
+  const nonstdDerivatives: FileTree[] = []
   fileTree.directories = fileTree.directories.filter((dir) => {
-    if (dir.name === 'derivatives') {
-      dir.directories.map((deriv) => {
-        if (
-          deriv.files.some(
-            (file: BIDSFile) => file.name === 'dataset_description.json',
-          )
-        ) {
-          derivatives.push(deriv)
-        }
-      })
+    if (dir.name !== 'derivatives') {
       return true
     }
-    return true
+    for (const deriv of dir.directories) {
+      if (
+        deriv.files.some(
+          (file: BIDSFile) => file.name === 'dataset_description.json',
+        )
+      ) {
+        // New root for the derivative dataset
+        deriv.parent = undefined
+        bidsDerivatives.push(deriv)
+      } else {
+        nonstdDerivatives.push(deriv)
+      }
+    }
+    // Remove derivatives from the main fileTree
+    return false
   })
 
   for await (const context of walkFileTree(fileTree, issues, dsContext)) {
@@ -111,7 +117,7 @@ export async function validate(
 
   let derivativesSummary: Record<string, ValidationResult> = {}
   await Promise.allSettled(
-    derivatives.map(async (deriv) => {
+    bidsDerivatives.map(async (deriv) => {
       derivativesSummary[deriv.name] = await validate(deriv, options)
       return derivativesSummary[deriv.name]
     }),