Fix window id plumbing, and restore native windows across a reload

[AllTerrainDeveloper]

Four bugs in how a window's id is resolved and persisted. All live on trunk.

1. iframeContent native windows bake the registered id

createRegisterWindow passes def.id into the synthesised render callback, but manager.open() reassigns the id whenever an instance of the same baseId is already open (chat → chat-2 — e.g. opening the same registered window on a second virtual desktop).

The second instance then registers its synthetic iframe, marks content ready, routes bridge messages, and dispatches window channels under the first instance's id:

• its loading overlay never clears
• connect( 'chat-2' ) finds no iframe and drops every message
• Window.on( channel ) never fires

The render now resolves the live instance id from the window root (wp-window-<id>) it mounts into.

2. iframeContent cleanups never run

onClose was wrapped only when cleanups.length was non-zero — but that array is populated by the render callback, which doesn't run until manager.open() hydrates the window. The check always saw an empty array, so the wrapper was never installed.

Every iframeContent window leaked a stale _syntheticIframes entry pointing at a detached iframe (which the next instance of that id would then find instead of its own) plus a message listener that stayed on window for the rest of the session. Now gated on def.iframeContent.

3. Session restore collapses duplicate instances

restoreSession replayed each saved window through open(), which matches on baseId. A session holding two instances of one page (edit-php + edit-php-2, both baseId edit-php) came back as one window, and when the two had been navigated apart the URL-aware reuse check dragged the survivor to the second window's URL — losing the first page too.

Restore now goes through openNew(), which always constructs. openNew() in turn honours a free caller-supplied instance id verbatim, so saved ids come back unchanged and anything keyed by window id (the saved focused-window pointer, per-window plugin state, wp.desktop.onWindow( id )) still lines up.

4. Native windows don't survive a reload

Open OS Settings, hit F5, it's gone. Same for Bug Report and for every window registered through desktop_mode_register_window().

Two places dropped them:

• snapshot() filtered out native: true before persisting, because a native window's render callback is a JS closure and can't be serialized. True, and beside the point — the closure never needed serializing, since every native window is addressable by id and the shell can ask its owner to reopen it.
• Even had the client sent them, the server discarded them: native windows carry a #slug marker instead of an admin URL, which fails the same-admin check guarding the restore path against foreign origins.

Native entries now persist with native: true. The server rebuilds the #slug marker from the sanitized id rather than storing the client's string — nothing navigates to it, so there's no reason to round-trip a client-controlled value through user meta. The same-admin gate is untouched for iframe windows.

Restore reopens them through a single openNativeWindowById dispatcher (built-in openers first, then the native-window registry) and skips ids nothing answers to — a plugin deactivated since the session was saved. Those openers build their own manager.open() config from the registry and have nowhere to put restore-time values, so restoreSession stages the saved geometry / desktop / state via the new WindowManager.seedWindowRestoreState(); the manager merges each entry into the first window claiming that id, then forgets it. A lifecycle-event barrier between opens keeps the saved stacking order and the focused-window restore deterministic despite the openers being fire-and-forget.

Ephemeral windows (editor previews, whose URLs carry single-use nonces) remain the one category that's never persisted.

Tests

• tests/vitest/native-window-iframe-content-id.test.ts — 5 tests, 4 fail without the fix
• tests/vitest/session-restore-duplicates.test.ts — 16 tests covering duplicate restore, openNew id allocation, native restore, and snapshot shape
• tests/phpunit/tests/desktopModeSession.php — 4 new: native entries survive sanitization, the marker is rebuilt from the id (a foreign url on a native entry is discarded), iframe windows keep the strict same-admin gate, and the native key stays absent for iframe windows
• Green: 2429 JS tests / 249 files, 1644 PHP tests. lint, typecheck, build clean.

Docs

• architecture.md — new "What comes back, and how" under Session persistence
• javascript-reference.md — openNew()'s id-allocation contract, seedWindowRestoreState()
• bridge-protocol.md — windowId in the synthetic-iframe section is the live instance id, not the registered one