feat: upstream extras (background sync, run code blocks, Codex instructions, polish)

[TheDarkPhantom]

Seven upstream t3code changes ported onto the fork, one commit each.

Landed

• feat(desktop): keep running threads synced in the background pingdotgg/t3code#13554 Running threads keep syncing in the background (desktop). RunningThreadKeepAlive is mounted in __root.tsx on Electron. It mounts the thread state atom only for threads whose session is starting or running, and keeps a stopped thread mounted until its own detail stream is live and shows the stop. The fork has no enabledEnvironmentIds, so the environment set comes from the connection catalog, the same set the shell atoms enumerate. Its identity only changes when an environment is added or removed. Test: apps/web/src/state/threads.test.ts.
• feat(web): run shell commands from chat in the thread terminal pingdotgg/t3code#13060 Run button on shell code blocks. Shows on finished, single-line sh/bash/zsh/fish/shell/powershell/pwsh fences in assistant messages. It types the command into the thread terminal through runProjectScript, using a ref so the callback stays stable and memoized rows don't re-render. The detection is in chat/runnableCodeBlock.ts with a focused test. It rejects multi-line blocks, trailing backslashes, and control or bidi characters. On Windows the terminal is pwsh, so a bash block runs there exactly as if you had pasted it. This matches upstream: there's no shell translation.
• fix(server): newer Codex models get T3 Code's instructions again pingdotgg/t3code#13547 Newer Codex models get Avi Code's instructions again. Runtime info and the collaborative browser guidance now go in turn/start.additionalContext (avi_code_runtime, avi_code_tools), which every model receives. The mode prompt stays in developer_instructions, so older models behave as before; upstream also sends both paths on every model. After a root thread compacts, the last context is re-injected with thread/inject_items. Child agent compactions are ignored. Not ported: upstream's device tool text, model display names, and RuntimeInstructions.ts.
• fix(clients): sync status no longer flickers when opening running threads pingdotgg/t3code#13551 Sync status no longer flickers. Adds the pure client-runtime/delayed-status helper and upstream's test, plus a useDelayedStatus hook around the ThreadSyncStatusPill phase in ChatView. Logic that depends on the real phase still reads threadSyncPhase.
• fix(web): sidebar Back always returns to the main app pingdotgg/t3code#13516 Back and Escape return to the main app. mainAppLocation.ts tracks the last main app URL. Settings, usage, the changelog route, and the settings sidebar Back button all go there.
• fix(web): new worktree threads no longer say "checkout" during setup pingdotgg/t3code#13590 No "Local checkout" during worktree setup. resolveEffectiveEnvMode takes preparingWorktree, and resolveLockedWorkspaceLabel takes the env mode. ChatView always passes its env mode to BranchToolbar. Logic tests are updated.
• fix(web): keep sidebar terminal pulses in sync pingdotgg/t3code#12962 Terminal pulses in sync. synchronizeTerminalPulse runs once when each animation starts (no timer, no frame loop). It's wired into SidebarV2, SidebarThreadRow, and ThreadStatusIndicators. The pulse is now motion-safe:.

Skipped

None.

Verification

• vp test run on every touched test file: 10 files, 165 tests pass.
• tsgo --noEmit for apps/web, apps/server, and packages/client-runtime: clean.
• vp lint and vp fmt on changed paths: clean. The remaining ChatMarkdown no-unstable-nested-components warnings were already there.
• vp run check:avicode and the parseChangelog test pass.
• Merged the latest origin/main, which includes chore: backport upstream desktop UI fixes (2026-09-29) #243 and chore: backport upstream server fixes (2026-09-29) #244. CHANGELOG keeps one ### Upstream t3code section under Unreleased.

No contract schema changes and no migrations.

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