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

[devin-ai-integration]

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

Summary

Changes the organization persister from storing all organizations in a single organizations.json file to storing each organization as an individual markdown file (organizations/<UUID>.md) with YAML frontmatter. This follows the same pattern established in PR #2791 for the human persister.

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.

New files:

• utils.ts - Path helpers and frontmatter parsing
• collect.ts - Write operation collector for frontmatter batch export
• load.ts - Load organizations from markdown files + orphan cleanup
• migrate.ts - Auto-migration from organizations.json on first load

Example output format:

---
created_at: "2024-01-01T00:00:00Z"
name: "Acme Corp"
user_id: "user-123"
---

Review & Testing Checklist for Human

• Migration safety: Verify the migration logic in migrate.ts correctly handles edge cases (empty JSON, malformed JSON, partial migration failures). The migration deletes organizations.json after migrating - confirm this is the desired behavior.
• Orphan cleanup correctness: Review cleanupOrphanOrganizationFiles in load.ts to ensure it won't accidentally delete valid organization files if validOrgIds is incorrectly populated.
• End-to-end test: Run the desktop app locally with existing organizations.json data and verify:
  1. Migration happens automatically on first load
  2. Organizations are readable after migration
  3. New organizations are saved as markdown files
  4. Deleted organizations have their files cleaned up

Notes

• The parseMarkdownWithFrontmatter function is duplicated from the human persister rather than shared - this matches the existing pattern but could be consolidated in a future refactor.
• All 236 desktop tests pass, including the rewritten organization persister tests.

Link to Devin run: https://app.devin.ai/sessions/9d5f79c14dcf49bb88c6ffac3866403b
Requested by: yujonglee (@yujonglee)

[devin-ai-integration]

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[graphite-app]

Critical: Potential data loss during migration

The migration skips if the organizations directory exists, even if it's empty or incomplete. This prevents re-migration if a previous migration failed partway through.

Scenario that breaks:

1. User has organizations.json with data
2. Migration starts and creates organizations directory
3. Migration fails before completing (crash, network issue, etc.)
4. On next startup, migration is skipped because directory exists
5. Data from organizations.json is never migrated

Fix:
Check if the directory is non-empty instead of just checking existence:

const dirExists = await exists(organizationsDir);
if (dirExists) {
  // Check if directory has any .md files before skipping
  const entries = await readDir(organizationsDir);
  const hasMdFiles = entries.some(e => !e.isDirectory && e.name.endsWith('.md'));
  if (hasMdFiles) {
    return; // Only skip if there are actual migrated files
  }
}

Suggested change

	const dirExists = await exists(organizationsDir);
	if (dirExists) {
	return;
	}
	const dirExists = await exists(organizationsDir);
	if (dirExists) {
	// Check if directory has any .md files before skipping
	const entries = await readDir(organizationsDir);
	const hasMdFiles = entries.some(e => !e.isDirectory && e.name.endsWith('.md'));
	if (hasMdFiles) {
	return; // Only skip if there are actual migrated files
	}
	}

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