refactor: second-pass sink-file and boundary governance

## Context

First-pass sink-file governance (#363) split `components.tsx`, `SettingsModal.tsx`, `ProvidersPanel.tsx`, `renderer/main.tsx`, and `main/main.ts`, and closed with the instruction to track a fresh second-pass scan in a follow-up issue. This is that issue.

A full-repo scan (38 area/file audit agents + per-finding adversarial verification against current `main`, calibrated with #363's rules) confirmed ~40 findings. As in #363, the problem is never file length by itself: every finding below is about unrelated responsibilities sharing one module, a broken verification boundary, a parallel implementation that can silently diverge, or a name/location that misleads. Large single-responsibility data/fixture/generated files were explicitly excluded.

## Headline evidence

- `apps/desktop/src/main/main.ts` regrew from 1663 lines (post #385) to 2412. `registerIpc()` is ~800 lines inlining ≥8 feature domains, while 11 sibling `*-ipc-main.ts` files already follow a `register*Ipc(deps)` pattern — the seam exists but was applied inconsistently. Its own contract test regex-matches raw source text because `registerIpc` runs as a module side effect and cannot be invoked in isolation: the verification boundary is already broken.
- `packages/headless/src/harbor-cell.ts` (1810 lines) fuses session orchestration, a ~600-line env→ContextBudgetPolicy compiler, subprocess/tool-executor plumbing, and credential resolution. `runtime-policy-ab-run.ts` imports one env-key list from it and drags in `node:child_process`, runtime backends, and credentials.json reading. 44 commits have touched this file for unrelated reasons.
- Security-relevant duplication: the filesystem-containment guards (`isContainedPath`/`isSafeSkillId`, `isInside`/`toRelative`) exist as byte-identical private copies in `packages/runtime/src/skills.ts`, `apps/desktop/src/main/explore-agent-tool.ts`, and `apps/desktop/src/main/managed-skill-sources.ts`. A future fix to the containment check must currently be applied in multiple places.

## PR mapping

- High and medium slices: one file, one PR — each checkbox below is one independently reviewable, independently revertible PR.
- Low-severity mechanical items: batched into two cleanup PRs (one per area) instead of one PR per one-line change.
- Every PR follows the worktree/branch convention; flat off `main`, no stacking.

## Order of work

1. The two high-severity sinks first (`main.ts`, `harbor-cell.ts`) plus the security-relevant guard dedup.
2. Remaining splits grouped by package, in parallel lanes (see Parallelization).
3. The two mechanical cleanup batches last (or whenever a lane frees up — they conflict with nothing outside their own files).

## Invariants

Same as #363: behavior- and visually-neutral; preserve public imports (keep re-export compatibility where a moved symbol is public); no reverse imports from new leaf files; co-migrate source-reading contract tests; flat PRs off `main`; proportional verification (typecheck/build + targeted contract tests for pure moves).

## Slices

### High

- [x] **`apps/desktop/src/main/main.ts`** — migrate the un-migrated `registerIpc()` domains (sessions, onboarding, settings/bots/network, permissions+capabilities+health, quickChat+expertTeam, gateway, workspaceInstructions, git, workspace search) into `register*Ipc(deps)` modules following the existing 11-file pattern; `registerIpc` becomes pure composition. The backing logic modules (`onboarding-service.ts`, `quick-chat.ts`, `expert-team-start.ts`, `permissions-actions.ts`, `capability-snapshot.ts`) already exist.
- [x] **`packages/headless/src/harbor-cell.ts`** — four-way split: context-budget env compiler → `harbor-cell-context-budget-env.ts`; tool executors + subprocess helpers → `harbor-cell-tool-executor.ts`; provider/credential resolution → merge into the existing `provider-env.ts` seam; `harbor-cell.ts` keeps orchestration + backend wiring. Also dedupe `booleanEnv`/`positiveIntEnv`/`numericEnv` into `headless-run-env.ts` (a third private copy lives in `harbor-task-runner.ts`).
- [x] **Containment-guard dedup (security)** — single shared home for `isContainedPath`/`isSafeSkillId` (runtime) and `isInside`/`toRelative` (desktop); `managed-skill-sources.ts` and `explore-agent-tool.ts` import instead of keeping byte-for-byte copies.

### packages/runtime

- [x] **`context-budget.ts` (3001)** — extract the history-compact block engine into `history-compact-*.ts` siblings and the full synthesis-cache subsystem into `synthesis-cache.ts` (pairing existing `synthesis-cache-artifacts.ts`); keep only budget shaping + orchestration hooks, with `context-budget.ts` as the compatibility export surface.
- [x] **`ai-sdk-backend.ts` (4347)** — extract the ~1800-line history-compaction/context-budget orchestrator (the `build*PrepareStep` family, mid-turn compaction, overflow recovery, compact/synthesis-cache load/write methods) into a dedicated collaborator; `AiSdkBackend` keeps the streamText↔event/permission adaptation. Land after the `context-budget.ts` split to avoid import churn.
- [ ] **`runtime-kernel.ts`** — extract the history-compact checkpoint cache/CAS-write/cleanup coordinator into a sibling next to `history-compact-checkpoint.ts`; resolve the private `AsyncEventQueue` duplicate against `async-queue.ts` (reuse or rename with documented contract difference).
- [x] **`tool-runtime.ts`** (done: #1214) — extract the ~270-line provider-error classification taxonomy (`classifyError`, regex tables, evidence normalization) into its own module.
- [ ] **`session-manager.ts`** (in flight: #1253, needs rebase after #1385) — extract branch-session creation + runtime-ledger cloning (~250 lines, own verification boundary) into `session-branch.ts`; import `headerLineage` from `agent-run-recovery.ts` instead of the verbatim copy.
- [ ] **`agent-run.ts`** — extract the prior-run context assembly (`buildPriorRuntimeContext` + repair/backfill helpers) into `prior-run-context.ts`; move the pure status-projection helpers into `session-projection-helpers.ts` where their siblings already live.
- [ ] **`skills.ts` (1189)** — split along the package's existing convention into discovery / scan / metadata / (remaining) modules, keeping the `@maka/runtime` public exports stable.
- [x] **`active-full-compact.ts`** (done: #1259) — extract the ~380-line regex fact-extraction engine (summary fields only) into a sibling file.
- [ ] **`computer-use-tools.ts` (1763)** — extract the wire-protocol codec (zod schemas, `adaptToCuAction`, `snapshotComputerParams`) mirroring `openai-computer-codec.ts`; move the `CuDispatchBackend`/`CuRunResult`/… contract types into a dedicated types module so adapters stop importing the implementation file.

### packages/headless

- [ ] **`prompt-candidate-loop.ts` (1007)** — extract the git safety/rollback wrapper and the trajectory/tool-failure digest extraction into siblings; dedupe the two hand-rolled "held-in task set hash" implementations (`rsi-round-analysis.ts` re-implements it and the outputs are compared with strict equality across the WAL boundary).
- [ ] **`task-agent-controller.ts`** — extract the permission-intervention decision engine into `permission-intervention.ts` beside `permission-grants.ts`.
- [ ] **`fixed-prompt-controller.ts`** (in flight: #1261, needs rebase after #1352) — extract the ~340 lines of WAL event schema types into `fixed-prompt-wal-types.ts`.

### packages/core + storage

- [x] **`core/settings.ts`** (done: #1265) — extract the bot-chat channel subsystem (types, defaults, ~250-line readiness state machine) into `bot-chat-settings.ts`; move the web-search credential-reconciliation logic into `web-search.ts`; resolve the `NetworkSettings` name collision with `settings/network-settings.ts`.
- [x] **`storage/settings-store.ts`** (done: #1266) — extract the usage-stats JSONL aggregation engine into a sibling `usage-stats-store.ts` that `SettingsStore` delegates to.
- [ ] **`core/local-memory.ts`** (blocked on #820 — coordinate before starting) — replace the embedded hand-rolled SHA-256 with the same digest-injection seam `oauth-subscription.ts` uses; collapse the duplicated meta-value sanitizer onto `normalizeMetaValue`.

### apps/desktop + cli + computer-use

- [x] **`preload/preload.ts`** (done: #1204) — define the `window.maka` bridge shape once and link `preload.ts` (`satisfies`) and `global.d.ts` to it (today they are two hand-maintained declarations with no compiler link); relocate the browser-API attachment encoder out of `src/main/` (preload's own header forbids main-process deps).
- [ ] **`cli/pi-tui-runner.ts`** — extract the shell-run hydration/buffering state machine into `shell-run-hydration.ts`.
- [ ] **`computer-use/cua-driver-backend.ts` (2701)** — extract the TOCTOU target staleness/occlusion re-verification into `cua-driver-target-resolution.ts`, mirroring `cua-driver-snapshot.ts`.

### Mechanical cleanup batches (low severity, one PR each)

- [ ] **Batch: core + runtime mechanical** (in flight: #1374, approved) — `semantic-compact.ts` reuses `request-shape.ts`'s exported `stableHash`/`stableStringify` instead of its local `sortJson`/`sha256` trio; move the generic `Result` helper from `core/settings/result.ts` to `@maka/core/result`.
- [ ] **Batch: desktop + ui mechanical** — rename `OnboardingHero.tsx`, `FirstRunChecklist.tsx`, `SettingsModal.tsx`, `ProvidersPanel.tsx` to kebab-case; replace `app-shell.tsx`'s hand-rolled pending-set with the `useKeyedPendingRegistry` hook it already uses four times; move the four authored Markdown skill bodies out of `main/skills.ts` into content files; extract `composer.tsx`'s self-contained workspace/branch-picker row into `composer-workspace-row.tsx` (mirroring `chat-model-switcher.tsx`) (done).

## Parallelization

All slices touch disjoint files except two ordered pairs, so the work splits into independent lanes that different contributors can pick up concurrently (one worktree + branch per slice):

- **Lane desktop** — `main.ts`, preload, desktop+ui mechanical batch (batch last; it shares `app-shell.tsx` import-line churn with nothing else).
- **Lane runtime/compaction** — `context-budget.ts` then `ai-sdk-backend.ts` (same feature family; sequence them under one owner to avoid import churn); `runtime-kernel.ts` is same-family but disjoint files, can go to a second owner.
- **Lane runtime/other** — `tool-runtime.ts`, `session-manager.ts`, `agent-run.ts`, `skills.ts`, `active-full-compact.ts`, `computer-use-tools.ts`: six disjoint files, up to six owners.
- **Lane headless** — `harbor-cell.ts`, `prompt-candidate-loop.ts`, `task-agent-controller.ts`, `fixed-prompt-controller.ts`: disjoint.
- **Lane core/storage** — `settings.ts`, `settings-store.ts`, `local-memory.ts`, core+runtime mechanical batch.
- **Lane cli/cua** — `pi-tui-runner.ts`, `cua-driver-backend.ts`.

Ordering constraints: (1) `context-budget.ts` split lands before the `ai-sdk-backend.ts` orchestrator extraction; (2) the containment-guard dedup and the `runtime/skills.ts` split both involve `skills.ts` — they compose cleanly as long as the `@maka/runtime` public exports stay stable, but prefer one owner for both.

## Borderline (evidence confirmed, worth-a-PR disputed — decide per slice, default skip)

- `cli/pi-transcript.ts`: pure transcript reducer vs ANSI rendering layer separation. **Declined after re-verification** — the toggle reducers and renderer are bidirectionally coupled through shared render geometry (`entryFirstLine`/`viewportTop`); no clean boundary.
- `core/settings.ts` `UsageRequestLog`/`UsageSummary` vs `usage-stats/types.ts` type overlap. **Moved out of scope** — two generations of the usage data model (Settings page v1 vs telemetry v2); needs its own migration issue, not a mechanical dedup.
- `headless/fixed-prompt-controller.ts`: second, production-unused Harbor result parser (`readHarborTaskRunOutput`). Suggested: fold into #1261 — demote to test-private or delete.
- `headless/ahe-evidence-export.ts`: evidence export vs target-snapshot building split. **Declined after re-verification** — export and target-snapshot building share one result type; split value is low.

## Out of scope

Same as #363: visual redesign, breaking public imports, splitting large single-purpose data files for line count, rewriting runtime behavior while moving files, new dependency/import-cycle tooling.

## References

- #363 first-pass sink-file governance (predecessor; closed with the instruction to open this follow-up).
- #385 `main/main.ts` first split (the `register*Ipc` pattern this issue extends).
- #1046 CSS/token governance (adjacent, separate track).

## Status update (2026-07-23)

A full re-verification against current `main` confirmed the remaining unclaimed slices are still valid; refreshed scopes now live in per-slice sub-issues (#1405–#1414) so they can be claimed individually. In-flight: #1253 and #1261 need a rebase; #1374 is approved. A third-pass full-repo scan found a new set of verified findings, tracked in #1404; source-regex extraction-contract test governance is tracked in #1403.

Choose one unchecked slice rather than the umbrella issue, then read its named source file and the analogous module or seam described in that slice, such as runtime-kernel.ts with async-queue.ts or main.ts with the existing register*Ipc files. Verify the chosen move with the stated typecheck/build and any targeted contract tests, preserving public imports, behavior, and the listed ordering or coordination constraints.

Written by the indexing model from the issue text.