Revert #4421 and narrow the cache restore fix

[boudra]

Reasoning

Revert #4421 because phone dogfooding produced a reordered conversation after its timeline reducer and persisted-cache rewrite. Restore the established reducer, retain the provider/native crash fixes, and fix cached baseline restoration at the existing restore owners.

Linked issue

Refs #4421, #4401, #4431. Related open work #4256 and #4153 addresses separate timeline problems and is not superseded.

Type of change

• Bug fix
• Docs

Goals

• Paint cached conversations and the complete cached workspace directory despite live updates during disk reads.
• Preserve the established timeline reconciliation and persisted format.
• Keep native model loading, appearance changes, and cold-start navigation working.

Non-goals

No replacement reducer, provenance fields, second timeline lane, new production module, queue, revision counter, or state machine. No changes after the revert to session-stream-reducers.ts, types/stream.ts, session-store.ts, or the cache codec/row format.

Four commits and evidence

Evidence root E = /tmp/revert-4421-evidence/, a symlink to this worktree's .dev/revert-4421-evidence/. Paths below are local artifacts retained for maintainer review.

Commit	Change	Production additions/deletions	Ignoring whitespace
5d1dd0580142a80968df5adc40b5d8d172078c0c	Plain squash revert	+2508 / −2840 = 5348	+2420 / −2752 = 5172
f5fdf0254bc2ad1a1856cd09448472af4dcd621e	Native AbortSignal.aborted + CancelledError	+3 / −3 = 6	6
b19628245beee0f55a65b09fb59b8889e00e1b22	Appearance boundaries below navigators, array transform origin, ready navigation intent	+139 / −64 = 203	+106 / −31 = 137
1e378c94c4114cd8ab89730ed4b76419fb6dcc96	Concurrent baseline reads; retain cached rows beneath live updates	+20 / −18 = 38	+13 / −11 = 24

Counts exclude tests/docs; E/commit-lines.json records them. Commits 2–4 total 247 raw changed lines / 167 ignoring whitespace. The maintainer explicitly approved exceeding the initial 150-line guard to retain the reproduced navigation crash fix.

1. Revert base was corrected to 8c89e72a0; 1c51b52d0 was verified as an ancestor. No revert conflicts; Restore body dragging for model and plugin sheets #4431's bottom-sheet gesture changes remain intact.
2. Provider test reproduced the missing native throwIfAborted; all 13 provider tests pass.
3. Back → launcher → agent deep link reproduced the Root Layout error on the reverted APK: E/baseline-deeplink-error.png, baseline-logcat.txt. Ready-intent test fails before and all 8 pass after (navigation-red.log and focused logs). Final journey passes: final-back-launcher.png, final-deeplink.png. Appearance placement 3, menu 18, explorer host 4 tests pass.
4. Real SQLite row adapter/cache tests reproduce display-only restoration and timeline/directory read ordering races: timeline-red.log, timeline-ordering-red.log, directory-red.log. Final viewed timeline 31, replica 14, directory 18 tests pass. The existing directory test proved that the checkpoint must still be withheld after a live revision; only checkpoint assignment retains that existing guard. Cache rows now merge beneath live state.

QA

CI green on 1e378c94c4114cd8ab89730ed4b76419fb6dcc96: all applicable checks, including all four Playwright shards, passed; review threads resolved. Final status evidence: E/ci-review.json.

• npm run typecheck, npm run lint, npm run format:check pass: E/final-typecheck.log, final-lint.log, final-format-check.log. npm run format ran before every commit/amend.
• Review follow-up: real SQLite diagnostic deletes an agent and workspace during the directory read and asserts a second storage read plus absence of both deleted rows. It passes on this head: E/directory-deletion-green.log, directory-deletion-diagnostic.test.ts. The existing cache host-revision check flushes mutations and rereads before returning; no new deletion tracking is needed.
• Focused Vitest files ran individually with --bail=1, including reverted reducer/store/cache/host/submission owners. Logs are retained under E; no full workspace suite ran.
• 102 unchanged Playwright cases pass, one worker: agent stream, viewed timelines, submission, pagination, resume, all New Workspace specs, and published 0.2.5 daemon pagination. E/playwright.log = 75; submission-passed.txt/playwright-quota-failure.log = 25; playwright-submission-remaining.log = 2.
• Release x86_64 APK built with APP_VARIANT=production EXPO_PUBLIC_LOCAL_DAEMON=localhost:6768, assembleRelease; installed on existing paseo-api35 emulator against the dev daemon on 6768 through a local response-delay proxy. E/android-final-build.log, final-apk.sha256, final.apk.

APK check	Result and observation	Evidence under E
Delayed reply	PASS: cached paint at 3.62s; reply at 13.02s, 9.40s later	check1-delayed.log, delayed-cached.png, qa-events.jsonl, proxy.jsonl
Offline paint and directory	PASS: history painted with both endpoint ports REJECTed; all 46 cached workspaces visible after Show more; none missing	check2-offline.log, offline-history.png, offline-sidebar-comparison.json, offline-sidebar-expanded-*.txt
Live event during read	PASS: five real live events during a 12s native SQLite pause; cached history and live content visible before delayed reply	check3-race.json, read-race-attached.log, race-after-read.png, race-after-read.db
Reopen order	PASS: app process stopped while this task streamed; all 40 persisted rows match their order in the daemon's 292-entry projected reply, including non-monotonic ending cursors	check4-order.json, daemon-projection.json, reopen-before.db, reopen-after.db, check4-reopened.png
Model selectors	PASS: existing agent list and New Workspace provider/model lists populate	check5-existing-models.png, check5-new-workspace-codex.png, new-model-list.txt
Appearance and five cold starts	PASS: interface size 15→16 committed, syntax menu opened; five distinct app PIDs painted history; zero native crash/Root Layout matches	font-committed.txt, check6-syntax-menu.png, check6-cold-starts.json, check6-cold-*.png, check6-logcat.txt, check6-crash-matches.txt

Codec behavior: rows written by #4421 containing source are rejected as cache misses and fall through to a normal fetch; older-format rows decode. SQLite diagnostic covered all ten original rows (five source-bearing, five older format): E/cache-diagnostics.log, cache-diagnostic.test.ts, original-4421-cache.db. Direct APK proof: one remaining 40-item source-bearing row fetched successfully and was replaced by 40 decodable items, with visible history and no permanent spinner: codec-native-result.json, codec-native-before.db, codec-native-after.db, codec-native-after.png.

Not fixed

The shared cache write queue can delay a host A read behind a host B write. Reproduced using the real SQLite adapter, left unfixed as explicitly requested: E/cache-diagnostics.log and E/cache-diagnostic.test.ts retain the failing-test evidence. No cache queue or codec changes are included.

Verification deviations and limits

• Approved line-count exception and conditional ready-intent inclusion are described above; exactly four commits remain.
• Revert used --no-commit so the required formatter could run before committing; its patch is the plain reverse of the squash commit.
• Shared /tmp quota exhaustion and browser process crashes interrupted one run. Evidence and temporary files moved onto the workspace disk; all incomplete/failed requested cases subsequently passed unchanged. No assertions, retries, or timeouts were weakened.
• Early Frida spawn instrumentation failed in the Android linker before SQLite. The successful race check attached after normal startup and paused the real SQLite read when opening an uncached-in-memory agent. The six normal native cold starts/deep-link checks ran without instrumentation. Instrumentation logs remain under E.
• The baseline repro APK packaging reused its already-built baseline bundle after an interrupted build; the final APK was rebuilt with all four commits.
• Android emulator and browser were exercised. iOS, physical devices, and Electron were not manually tested. Configured Copilot and slow-test providers returned their own errors; working providers populated successfully.
• Neither daemon on 6768/6767 was restarted; /tmp/replica-4160 was not modified. No other model was started or delegated work.

Checklist

• One focused change
• npm run typecheck passes
• npm run lint passes
• npm run format passes
• QA evidence
• Tests added or updated where it made sense

[greptile-apps]

Greptile Summary

This PR reverts the broad timeline/cache architecture from #4421 while retaining narrower native provider, appearance, navigation-readiness, and concurrent cache-baseline fixes.

• Restores the established timeline reducer, session projection, and persisted cache format.
• Moves cache preparation back to existing directory and viewed-timeline owners.
• Preserves native provider cancellation compatibility and navigator identity across appearance changes.
• Adds route-level cached workspace/agent preparation and ready-time navigation intent handling.
• Contains a directory-cache race that can resurrect rows deleted while the baseline read is pending.
• Weakens two asynchronous browser assertions by replacing polling with immediate samples.

Confidence Score: 4/5

The PR is not safe to merge until deleted rows cannot be resurrected by a late bulk cache read and the explicit deterministic-E2E requirement is restored.

A live deletion during the directory SQLite read can be undone by the subsequent cached-map merge, leaving the removed entity visible until a later demanded refresh; two browser tests also lost required retry behavior around asynchronous UI state.

Files Needing Attention: packages/app/src/runtime/directory-sync/index.ts, packages/app/src/runtime/directory-sync/agent-replica.ts, packages/app/src/runtime/directory-sync/workspace-replica.ts, packages/app/e2e/browser/sidebar-model-b.spec.ts, packages/app/e2e/browser/composer-autocomplete.spec.ts

Important Files Changed

Filename	Overview
packages/app/src/runtime/directory-sync/index.ts	Restores demand-driven directory ownership and concurrent baseline reads, but commits stale cached rows after live deletions.
packages/app/src/runtime/directory-sync/agent-replica.ts	Reverts agent directory lifetime integration and adds targeted cache-read tokens; bulk cached merges cannot retain deletion knowledge.
packages/app/src/runtime/directory-sync/workspace-replica.ts	Adds targeted workspace cache admission while bulk merges preserve live values but can reinsert deleted cached keys.
packages/app/src/timeline/viewed-timeline-sync.ts	Restores the established timeline owner and merges cached baselines beneath live observations.
packages/app/src/contexts/session-context.tsx	Rewires timeline response handling and transport ownership into the session bridge.
packages/app/src/navigation/themed-stack.tsx	Places appearance remount boundaries below native navigators to preserve navigator identity.
packages/app/src/navigation/workspace-route-navigation.ts	Retains the latest workspace navigation intent until the root navigation container is ready.
packages/app/src/data/providers-snapshot.ts	Uses React Query cancellation errors with native-compatible AbortSignal.aborted checks.
packages/app/e2e/browser/sidebar-model-b.spec.ts	Replaces an eventual tab assertion with an immediate snapshot, introducing hydration-timing sensitivity.
packages/app/e2e/browser/composer-autocomplete.spec.ts	Replaces polling of animation-dependent stacking state with a single immediate sample.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  Disk[Cached directory read] --> Merge[Commit cached baseline]
  Live[Live directory update] --> Current[Current session directory]
  Delete[Live deletion] --> Current
  Current --> Merge
  Merge -->|Present keys override cache| Updated[Updated live rows retained]
  Merge -->|Deleted key absent from current map| Resurrected[Cached deleted row reinserted]
  Resurrected --> UI[Directory/sidebar state]
  Refresh[Later demanded network refresh] -->|Eventually removes row| UI

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