refactor(desktop): store organizations as markdown files with YAML frontmatter

- Change organization persister from JSON to markdown files with frontmatter
- Store each organization as organizations/<UUID>.md
- Add auto-migration from organizations.json on first load
- Add cleanup of orphan files when records are deleted
- Follow the same pattern as the human persister from PR #2791

Organization schema fields (user_id, created_at, name) are stored in
YAML frontmatter. The markdown body is always empty since organizations
have no memo field.

Co-Authored-By: yujonglee <yujonglee.dev@gmail.com>

Author: devin-ai-integration[bot]

apps/desktop/src/store/tinybase/persister/organization/collect.ts

@@ -0,0 +1,55 @@
+import type { MergeableStore, OptionalSchemas } from "tinybase/with-schemas";
+
+import type { FrontmatterInput, JsonValue } from "@hypr/plugin-export";
+import type { OrganizationStorage } from "@hypr/store";
+
+import type { CollectorResult, TablesContent } from "../utils";
+import { getOrganizationDir, getOrganizationFilePath } from "./utils";
+
+export interface OrganizationCollectorResult extends CollectorResult {
+  validOrgIds: Set<string>;
+}
+
+type OrganizationsTable = Record<string, OrganizationStorage>;
+
+export function collectOrganizationWriteOps<Schemas extends OptionalSchemas>(
+  _store: MergeableStore<Schemas>,
+  tables: TablesContent,
+  dataDir: string,
+): OrganizationCollectorResult {
+  const dirs = new Set<string>();
+  const operations: CollectorResult["operations"] = [];
+  const validOrgIds = new Set<string>();
+
+  const organizationsDir = getOrganizationDir(dataDir);
+  dirs.add(organizationsDir);
+
+  const organizations =
+    (tables as { organizations?: OrganizationsTable }).organizations ?? {};
+
+  const frontmatterItems: [FrontmatterInput, string][] = [];
+
+  for (const [orgId, org] of Object.entries(organizations)) {
+    validOrgIds.add(orgId);
+
+    const frontmatter: Record<string, JsonValue> = {
+      created_at: org.created_at ?? "",
+      name: org.name ?? "",
+      user_id: org.user_id ?? "",
+    };
+
+    const body = "";
+    const filePath = getOrganizationFilePath(dataDir, orgId);
+
+    frontmatterItems.push([{ frontmatter, content: body }, filePath]);
+  }
+
+  if (frontmatterItems.length > 0) {
+    operations.push({
+      type: "frontmatter-batch",
+      items: frontmatterItems,
+    });
+  }
+
+  return { dirs, operations, validOrgIds };
+}

apps/desktop/src/store/tinybase/persister/organization/load.ts

@@ -0,0 +1,99 @@
+import { readDir, readTextFile, remove } from "@tauri-apps/plugin-fs";
+
+import type { OrganizationStorage } from "@hypr/store";
+
+import { isFileNotFoundError, isUUID } from "../utils";
+import {
+  getOrganizationDir,
+  getOrganizationFilePath,
+  parseMarkdownWithFrontmatter,
+} from "./utils";
+
+export async function loadAllOrganizations(
+  dataDir: string,
+): Promise<Record<string, OrganizationStorage>> {
+  const result: Record<string, OrganizationStorage> = {};
+  const organizationsDir = getOrganizationDir(dataDir);
+
+  let entries: { name: string; isDirectory: boolean }[];
+  try {
+    entries = await readDir(organizationsDir);
+  } catch (error) {
+    if (isFileNotFoundError(error)) {
+      return result;
+    }
+    throw error;
+  }
+
+  for (const entry of entries) {
+    if (entry.isDirectory) continue;
+    if (!entry.name.endsWith(".md")) continue;
+
+    const orgId = entry.name.replace(/\.md$/, "");
+    if (!isUUID(orgId)) {
+      console.warn(
+        `[OrganizationPersister] Skipping non-UUID file: ${entry.name}`,
+      );
+      continue;
+    }
+
+    try {
+      const filePath = getOrganizationFilePath(dataDir, orgId);
+      const content = await readTextFile(filePath);
+      const { frontmatter } = await parseMarkdownWithFrontmatter(content);
+
+      result[orgId] = {
+        user_id: String(frontmatter.user_id ?? ""),
+        created_at: String(frontmatter.created_at ?? ""),
+        name: String(frontmatter.name ?? ""),
+      };
+    } catch (error) {
+      console.error(
+        `[OrganizationPersister] Failed to load organization ${orgId}:`,
+        error,
+      );
+      continue;
+    }
+  }
+
+  return result;
+}
+
+export async function cleanupOrphanOrganizationFiles(
+  dataDir: string,
+  validOrgIds: Set<string>,
+): Promise<void> {
+  const organizationsDir = getOrganizationDir(dataDir);
+
+  let entries: { name: string; isDirectory: boolean }[];
+  try {
+    entries = await readDir(organizationsDir);
+  } catch (error) {
+    if (isFileNotFoundError(error)) {
+      return;
+    }
+    throw error;
+  }
+
+  for (const entry of entries) {
+    if (entry.isDirectory) continue;
+    if (!entry.name.endsWith(".md")) continue;
+
+    const orgId = entry.name.replace(/\.md$/, "");
+    if (!isUUID(orgId)) continue;
+
+    if (!validOrgIds.has(orgId)) {
+      try {
+        const filePath = getOrganizationFilePath(dataDir, orgId);
+        await remove(filePath);
+      } catch (error) {
+        if (!isFileNotFoundError(error)) {
+          console.error(
+            `[OrganizationPersister] Failed to remove orphan file ${entry.name}:`,
+            error,
+          );
+        }
+      }
+    }
+  }
+}

apps/desktop/src/store/tinybase/persister/organization/migrate.ts

@@ -0,0 +1,77 @@
+import { sep } from "@tauri-apps/api/path";
+import { exists, mkdir, readTextFile, remove } from "@tauri-apps/plugin-fs";
+
+import {
+  commands as exportCommands,
+  type FrontmatterInput,
+  type JsonValue,
+} from "@hypr/plugin-export";
+import type { OrganizationStorage } from "@hypr/store";
+
+import { isFileNotFoundError } from "../utils";
+import { getOrganizationDir, getOrganizationFilePath } from "./utils";
+
+export async function migrateOrganizationsJsonIfNeeded(
+  dataDir: string,
+): Promise<void> {
+  const organizationsJsonPath = [dataDir, "organizations.json"].join(sep());
+  const organizationsDir = getOrganizationDir(dataDir);
+
+  const jsonExists = await exists(organizationsJsonPath);
+  if (!jsonExists) {
+    return;
+  }
+
+  const dirExists = await exists(organizationsDir);
+  if (dirExists) {
+    return;
+  }
+
+  console.log(
+    "[OrganizationPersister] Migrating from organizations.json to organizations/*.md",
+  );
+
+  try {
+    const content = await readTextFile(organizationsJsonPath);
+    const organizations = JSON.parse(content) as Record<
+      string,
+      OrganizationStorage
+    >;
+
+    await mkdir(organizationsDir, { recursive: true });
+
+    const batchItems: [FrontmatterInput, string][] = [];
+
+    for (const [orgId, org] of Object.entries(organizations)) {
+      const frontmatter: Record<string, JsonValue> = {
+        created_at: org.created_at ?? "",
+        name: org.name ?? "",
+        user_id: org.user_id ?? "",
+      };
+
+      const body = "";
+      const filePath = getOrganizationFilePath(dataDir, orgId);
+
+      batchItems.push([{ frontmatter, content: body }, filePath]);
+    }
+
+    if (batchItems.length > 0) {
+      const result = await exportCommands.exportFrontmatterBatch(batchItems);
+      if (result.status === "error") {
+        throw new Error(
+          `Failed to export migrated organizations: ${result.error}`,
+        );
+      }
+    }
+
+    await remove(organizationsJsonPath);
+
+    console.log(
+      `[OrganizationPersister] Migration complete: ${Object.keys(organizations).length} organizations migrated`,
+    );
+  } catch (error) {
+    if (!isFileNotFoundError(error)) {
+      console.error("[OrganizationPersister] Migration failed:", error);
+    }
+  }
+}