Make startup deletion check more robust

frontend/obsidian-plugin/src/obsidian-file-system.ts

@@ -15,7 +15,27 @@ export class ObsidianFileSystemOperations implements FileSystemOperations {
 	) {}
 
 	public async listAllFiles(): Promise<RelativePath[]> {
-		return this.vault.getFiles().map((file) => file.path);
+		// Let's implement this by hand because vault.adapter.listAllFiles doesn't always return all files.
+		const allFiles = [];
+		const remainingFolders = [this.vault.getRoot().path];
+
+		// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+		while (true) {
+			const folder = remainingFolders.pop();
+			if (folder == undefined) {
+				break;
+			}
+
+			if (folder.includes(".obsidian")) {
+				continue;
+			}
+
+			const files = await this.vault.adapter.list(normalizePath(folder));
+			allFiles.push(...files.files);
+			remainingFolders.push(...files.folders);
+		}
+
+		return allFiles;
 	}
 
 	public async read(path: RelativePath): Promise<Uint8Array> {

frontend/sync-client/src/sync-operations/syncer.ts

@@ -1,6 +1,7 @@
 import type {
 	Database,
 	DocumentId,
+	DocumentRecord,
 	RelativePath
 } from "../persistence/database";
 import type { SyncService } from "../services/sync-service";
@@ -434,9 +435,16 @@ export class Syncer {
 
 		const allLocalFiles = await this.operations.listAllFiles();
 
-		let locallyPossiblyDeletedFiles = [
-			...this.database.resolvedDocuments
-		].filter(({ relativePath }) => !allLocalFiles.includes(relativePath));
+		let locallyPossiblyDeletedFiles: DocumentRecord[] = [];
+
+		for (const document of this.database.resolvedDocuments) {
+			if (
+				!document.isDeleted &&
+				!(await this.operations.exists(document.relativePath))
+			) {
+				locallyPossiblyDeletedFiles.push(document);
+			}
+		}
 
 		const updates = Promise.all(
 			allLocalFiles.map(async (relativePath) => {