Route application filesystem I/O through FileOperations

[franknoirot]

Closes #12350 by routing application-facing filesystem reads and mutations through the FileOperations coordination service introduced in #13628. This is the one-step production cutover: production application code no longer calls its filesystem-operation methods directly, which is why the PR's so many files (sorry!). In the next PR in the stack we introduce a pair of ESLint rules so that no new calls can ever be reintroduced.

1. Resolves FileOperations at registry-aware composition roots and passes it explicitly into registry-agnostic modules such as desktop.ts; those modules do not reach into the registry themselves.
2. Cuts desktop helpers, auth/settings persistence, project libraries, route loading, exports, keymaps, screenshots, telemetry, Zookeeper history, and other application consumers over to coordinated reads and writes.
3. Routes publication and cloud duplicate-manifest scans through coordinated reads. The cloud-sync engine keeps its private backing proxy because that proxy is the subsystem adapter that observes local mutations.
4. Preserves existing permission checks, file metadata, and case-only rename behavior using the access and stat capabilities established in Introduce Effect filesystem capabilities #13597 and coordinated in Add file operation coordinator to the registry #13628.
5. Applies the direct-fsZds I/O lint rule across production src and keeps the lower-level FileSystem adapter inaccessible to application consumers.

This does not delete systemIOActor: it still owns workflow concerns such as navigation and editor/project state. It does make FileOperations the single application-facing filesystem boundary, so removing those remaining workflow responsibilities can happen independently.

How to test

This is an important one to test! This is where the rubber hits the road. Exercise project and file workflows on both desktop and web: create, rename, move, duplicate, publish, and delete projects; create/edit/move/delete nested files and directories; export a project or screenshot; restart and confirm settings/keybindings persist. Behavior should remain unchanged while overlapping operations are coordinated by the shared service.

[vercel]

The latest updates on your projects. Learn more about Vercel for GitHub.

Project	Deployment	Actions	Updated
modeling-app	Ready	Preview	Sep 5, 2026 12:08am UTC

[franknoirot]

Drive-by deflake cop-out. The race is with navigation which I'll be addressing very soon.

[franknoirot]

I'll do some more self-review on Tuesday.

[franknoirot]

I think eventually I'd like the whole app to not use helpers like this, but rather just drop functionality if the fileOperations extension is not available. But we have to get basically everything into the registry system for that to work.