ENG-1629: Fix relations.json scattered across multiple locations (#947)

* ENG-1629: Fix relations.json scattered across multiple locations

Make vault root the canonical location for relations.json (always
"relations.json" at root, never under nodesFolderPath). Add a
one-time merge on plugin load to consolidate any scattered copies
left behind from previous nodesFolderPath changes.

Co-Authored-By: Claude Sonnet 4.6 (1M context) <noreply@anthropic.com>

* Fix early return when single relations.json exists at non-root path

Co-Authored-By: Claude Sonnet 4.6 (1M context) <noreply@anthropic.com>

* process root last

* Update apps/obsidian/src/utils/relationsStore.ts

Co-authored-by: graphite-app[bot] <96075541+graphite-app[bot]@users.noreply.github.com>

---------

Co-authored-by: Claude Sonnet 4.6 (1M context) <noreply@anthropic.com>
Co-authored-by: graphite-app[bot] <96075541+graphite-app[bot]@users.noreply.github.com>

Author: 3 people

apps/obsidian/src/index.ts

@@ -33,7 +33,10 @@ import { InlineNodeTypePicker } from "~/components/InlineNodeTypePicker";
 import { initializeSupabaseSync } from "~/utils/syncDgNodesToSupabase";
 import { FileChangeListener } from "~/utils/fileChangeListener";
 import generateUid from "~/utils/generateUid";
-import { migrateFrontmatterRelationsToRelationsJson } from "~/utils/relationsStore";
+import {
+  migrateFrontmatterRelationsToRelationsJson,
+  mergeAllRelationsJsonToRoot,
+} from "~/utils/relationsStore";
 
 export default class DiscourseGraphPlugin extends Plugin {
   settings: Settings = { ...DEFAULT_SETTINGS };
@@ -46,6 +49,10 @@ export default class DiscourseGraphPlugin extends Plugin {
   async onload() {
     await this.loadSettings();
 
+    await mergeAllRelationsJsonToRoot(this).catch((error) => {
+      console.error("Failed to merge relations.json files:", error);
+    });
+
     await migrateFrontmatterRelationsToRelationsJson(this).catch((error) => {
       console.error("Failed to migrate frontmatter relations:", error);
     });

apps/obsidian/src/utils/relationsStore.ts

@@ -3,7 +3,6 @@ import { uuidv7 } from "uuidv7";
 import type { DGSupabaseClient } from "@repo/database/lib/client";
 import type DiscourseGraphPlugin from "~/index";
 import { ensureNodeInstanceId } from "~/utils/nodeInstanceId";
-import { checkAndCreateFolder } from "~/utils/file";
 import { getVaultId, getLocalSpaceUri } from "./supabaseContext";
 import type { RelationInstance } from "~/types";
 import { QueryEngine, getImportedNodesRaw } from "~/services/QueryEngine";
@@ -14,13 +13,9 @@ import { getSpaceIdsBySpaceUris } from "./spaceFromRid";
 const RELATIONS_FILE_NAME = "relations.json";
 const RELATIONS_FILE_VERSION = 1;
 
-/** Vault-relative path for relations.json, under the same folder as nodes (nodesFolderPath). */
-export const getRelationsFilePath = (plugin: DiscourseGraphPlugin): string => {
-  const folderPath = plugin.settings.nodesFolderPath.trim();
-  return folderPath
-    ? normalizePath(`${folderPath}/${RELATIONS_FILE_NAME}`)
-    : normalizePath(RELATIONS_FILE_NAME);
-};
+/** Vault-relative path for relations.json — always at vault root. */
+export const getRelationsFilePath = (): string =>
+  normalizePath(RELATIONS_FILE_NAME);
 
 export type RelationsFile = {
   version: number;
@@ -37,7 +32,7 @@ const defaultRelationsFile = (): RelationsFile => ({
 export const loadRelations = async (
   plugin: DiscourseGraphPlugin,
 ): Promise<RelationsFile> => {
-  const path = getRelationsFilePath(plugin);
+  const path = getRelationsFilePath();
   const file = plugin.app.vault.getAbstractFileByPath(path);
   if (!file || !(file instanceof TFile)) {
     return defaultRelationsFile();
@@ -67,11 +62,7 @@ export const saveRelations = async (
   plugin: DiscourseGraphPlugin,
   data: RelationsFile,
 ): Promise<void> => {
-  const folderPath = plugin.settings.nodesFolderPath.trim();
-  if (folderPath) {
-    await checkAndCreateFolder(folderPath, plugin.app.vault);
-  }
-  const path = getRelationsFilePath(plugin);
+  const path = getRelationsFilePath();
   const toWrite: RelationsFile = {
     ...data,
     lastModified: Date.now(),
@@ -85,6 +76,56 @@ export const saveRelations = async (
   }
 };
 
+/**
+ * On plugin load, finds all relations.json files in the vault and merges them
+ * into the canonical location at vault root, then deletes the non-root copies.
+ * Handles the case where a user changed nodesFolderPath, leaving old files behind.
+ */
+export const mergeAllRelationsJsonToRoot = async (
+  plugin: DiscourseGraphPlugin,
+): Promise<void> => {
+  const allFiles = plugin.app.vault.getFiles();
+  const relationsFiles = allFiles.filter((f) => f.name === RELATIONS_FILE_NAME);
+  const rootPath = normalizePath(RELATIONS_FILE_NAME);
+  const nonRootFiles = relationsFiles.filter((f) => f.path !== rootPath);
+
+  if (nonRootFiles.length === 0) return;
+
+  // Process non-root files first so root values win on duplicate IDs.
+  const sortedFiles = [
+    ...nonRootFiles,
+    ...relationsFiles.filter((f) => f.path === rootPath),
+  ];
+  const merged = defaultRelationsFile();
+  const validatedNonRootFiles: TFile[] = [];
+  for (const file of sortedFiles) {
+    try {
+      const content = await plugin.app.vault.read(file);
+      const data = JSON.parse(content) as RelationsFile;
+      if (
+        typeof data.version !== "number" ||
+        typeof data.relations !== "object" ||
+        data.relations === null
+      )
+        continue;
+      Object.assign(merged.relations, data.relations);
+      merged.lastModified = Math.max(
+        merged.lastModified,
+        data.lastModified ?? 0,
+      );
+      if (file.path !== rootPath) validatedNonRootFiles.push(file);
+    } catch {
+      // skip unreadable or unparseable files
+    }
+  }
+
+  await saveRelations(plugin, merged);
+
+  for (const file of validatedNonRootFiles) {
+    await plugin.app.vault.delete(file);
+  }
+};
+
 export type AddRelationParams = {
   type: string;
   source: string;