@neuralis/brain-core 0.2.0 → 0.3.0

package/app/filesystem/ui/PendingReviewDialog.tsx

@@ -19,6 +19,8 @@ import { DiffView } from '../../cards/DiffView';
 import { detectLanguage } from '../../cards/diffUtils';
 import type { VisibleDiffQueue } from '../hooks/useVisibleDiffCards';
 import { acceptsAbsence, classifyReviewOutcome, hunksOf, type ReviewOutcome } from './pendingChangesModel';
+import { useFilesystemStore } from '../store/filesystemStore';
+import type { PackageApi } from '@neuralis/package-system/client';
 
 export type ReviewAction = 'approve' | 'dismiss' | 'revert';
 export type ReviewRequest =
@@ -42,13 +44,13 @@ const OUTCOME: Record<ReviewOutcome, { label: string; tone: string }> = {
 export type ReviewResult = { id: string; uri: string; action: ReviewAction; outcome: ReviewOutcome; detail?: string };
 
 /** Run one review verb with the record's own fingerprint; never throws. */
-export async function applyReview(params: { agentId: string; projectId: string | null }, rec: PendingChangeRecord,
+export async function applyReview(params: { agentId: string; projectId: string | null; client: PackageApi }, rec: PendingChangeRecord,
   preview: PendingPreview, action: ReviewAction, acknowledge: boolean): Promise<ReviewResult> {
   const body = { agentId: params.agentId, ...(params.projectId ? { projectId: params.projectId } : {}), id: rec.id,
     expectedFingerprint: preview.expectedFingerprint, ...(acknowledge ? { acknowledgeCurrentState: true as const } : {}) };
   try {
-    const result = action === 'approve' ? await approveFileReview({ ...body, uri: rec.uri })
-      : action === 'revert' ? await revertPendingChange(body) : await dismissPendingChange(body);
+    const result = action === 'approve' ? await approveFileReview({ ...body, uri: rec.uri }, params.client)
+      : action === 'revert' ? await revertPendingChange(body, params.client) : await dismissPendingChange(body, params.client);
     if (result && result.ok === false) {
       const detail = 'error' in result && result.error ? String(result.error) : 'Review refused';
       return { id: rec.id, uri: rec.uri, action, outcome: classifyReviewOutcome(detail), detail };
@@ -90,6 +92,7 @@ export function PendingReviewDialog({ request, agentId, projectId, run, onClose,
   /** Records still waiting outside this batch; `onNext` (given this batch's ids) opens the next one. */
   next?: number; onNext?: (batch: string[]) => void;
 }): React.ReactElement | null {
+  const client = useFilesystemStore((s) => s.client);
   const records = useMemo(() => request.kind === 'single' ? [request.rec] : request.records, [request]);
   const [previews, setPreviews] = useState<Record<string, PendingPreview | Error>>(
     () => request.kind === 'single' && request.preview ? { [request.rec.id]: request.preview } : {});
@@ -104,7 +107,7 @@ export function PendingReviewDialog({ request, agentId, projectId, run, onClose,
     const seq = (loads.current.get(rec.id) ?? 0) + 1;
     loads.current.set(rec.id, seq);
     const current = () => mounted.current && loads.current.get(rec.id) === seq;
-    const load = () => previewPendingChange({ agentId, ...(projectId ? { projectId } : {}), id: rec.id });
+    const load = () => previewPendingChange({ agentId, ...(projectId ? { projectId } : {}), id: rec.id }, client);
     void (again && refetch ? refetch(rec) : run(load, current))
       .then(preview => { if (current() && preview) setPreviews(p => ({ ...p, [rec.id]: preview })); },
         error => { if (current()) setPreviews(p => ({ ...p, [rec.id]: error instanceof Error ? error : new Error('Preview failed') })); });
@@ -140,7 +143,7 @@ export function PendingReviewDialog({ request, agentId, projectId, run, onClose,
     for (const rec of targets) {
       const preview = previews[rec.id];
       if (!preview || preview instanceof Error || results[rec.id]?.outcome === 'ok') continue;
-      const result = await applyReview({ agentId, projectId }, rec, preview, action, preview.requiresAcknowledgement.length > 0);
+      const result = await applyReview({ agentId, projectId, client }, rec, preview, action, preview.requiresAcknowledgement.length > 0);
       done.push(result);
       setResults(r => ({ ...r, [rec.id]: result }));
       // The state moved under the preview: fetch ONE fresh preview for this record

package/app/filesystem/ui/README.md

@@ -25,9 +25,9 @@ Re-exported from `app/filesystem/ui/index.ts`:
   - **`DiffModeToggle`** is the ONE Auto/Unified/Split control bound to the store `diffViewMode`, shared by BOTH the review diff AND the git diff (Auto picks unified/split by container width via `useContainerWidth`).
   - The editor also carries the VS Code-style **git left-gutter** (`codeEditor/editorGitGutter.ts` + the pure `codeEditor/gitLineStatus.ts` parser) for git-tracked files — a thin emerald(added)/blue(modified) bar + red delete caret, derived **fail-soft** from `getGitDiff({staged:false})` (Working↔Index).
   - `DiffView` (the old hand-rolled Myers review diff) was **DELETED** — superseded by `ReviewDiffView`. NB `app/cards/DiffView.tsx` is a DIFFERENT file (the chat-card single-column diff) and stays.
-- `Toolbar` — top toolbar with the active agent’s standalone configured icon (no visible name or identity badge), sidebar toggle, refresh, upload, and panel switches. The Changes switch carries the caller's visible pending COUNT as a static badge (`pendingCount`, the server `count_only` answer — `1000+` at the listing cap); the client `pendingReviewPaths` set only tones tree rows.
+- `Toolbar` — top toolbar with the active agent’s standalone configured icon (no visible name or identity badge), sidebar toggle, refresh, upload, and panel switches. The Changes switch carries the caller's visible pending COUNT as a static badge (`pendingCount`, the server `count_only` answer — `1000+` display cap; partial totals carry `+`, stale/unavailable totals `?`); the client `pendingReviewPaths` set only tones tree rows.
 - `SourcesPanel`, `PackagesPanel`, `VectorHealthPanel`, `PanelScaffold` — right-hand panels. Sources offers advisory metrics exclusions only when enabling an attested own data source with no sync block; Save persists the editable draft. Media summaries include local structural PNG failures, and chunk-only cleanup refreshes Files separately from removed-file counts.
-- `PendingChangesPanel` — Changes groups current Git status and pending review by source/repository, including non-Git sources. Normalized URI joining renders a file once while retaining separately labeled staged/unstaged comparisons for each overlapping repository and one pending review. All cards start expanded in ONE `useVirtualizer` list (`pendingChangesModel.ts` owns the filters, the flat row list, `rowEstimate`/`isMeasuredRow` and the Approve split; the compact row pins `h-8`, every card is measured; `overflow-anchor:none` plus an above-the-fold size adjustment keep the view still); the content lanes cache every loaded preview/diff, and source revisions plus context sequences fence obsolete replies. A **Type** filter (all · pending · Git) narrows the layers; the repository picker uses the Git panel's `resolveRepoLabel`. **Approve N** counts records with no acknowledgement on their own fields (`ackHintFor`, the server preview's own predicate) or in an already-loaded preview (`splitApprovable`'s `knownPreview`, no fetch of its own); the rest open `PendingReviewDialog` grouped by reason, each record sent with its own fingerprint, and every sweep reports a per-record result row (a refused revert included) — a record the sweep found needing an acknowledgement is reported AND handed to that grouped dialog (approve or dismiss with the acknowledgement). A batch (the sweep, a dialog group) HOLDS the source revisions its own writes bump (`holdRevisions`, released in `afterMutation`): N writes cost N verb requests, ONE re-list and at most one re-preview per card still listed — never a re-list plus every visible card's re-preview per write. A `changed` answer (`PENDING_STATE_CHANGED` / `PENDING_GENERATION_CHANGED`) is not final: the dialog fetches ONE fresh preview for that record (per-record sequence, liveness cleared on unmount only) and waits for a new click — never a replay. In the panel that ONE fetch is the panel's `refetch`: it waits for the re-list, the record's card holds meanwhile and adopts the answer under its final key (`takeRefetch`), so the card sends nothing of its own; a direct (dialog-less) refusal bumps only that card's preview nonce. A confirmed absence with a saved baseline is named in the preview body (`acceptsAbsence`). The orphan probe runs on mount, Refresh and Repair only — a source revision re-reads the plain list. Source inventory is separate from content, completed siblings are cached, truncation is shown, and Git errors do not hide other sources. Review reads a bounded pending preview/fingerprint with typed current/baseline/index states; ack-required state opens an explicit confirmation. Actual WRITE access gates card, compact, bulk and repair controls; historical cards remain read-only. Orphan ids arrive with the same pending listing, so Repair remains orphan-only and re-authorized server-side.
+- `PendingChangesPanel` — Changes groups current Git status and pending review by source/repository, including non-Git sources. Normalized URI joining renders a file once while retaining separately labeled staged/unstaged comparisons for each overlapping repository and one pending review. All cards start expanded in ONE `useVirtualizer` list (`pendingChangesModel.ts` owns the filters, the flat row list, `rowEstimate`/`isMeasuredRow` and the Approve split; the compact row pins `h-8`, every card is measured; `overflow-anchor:none` plus an above-the-fold size adjustment keep the view still); the content lanes cache every loaded preview/diff, and source revisions plus context sequences fence obsolete replies. A **Type** filter (all · pending · Git) narrows the layers; the repository picker uses the Git panel's `resolveRepoLabel`. **Approve N** counts records with no acknowledgement on their own fields (`ackHintFor`, the server preview's own predicate) or in an already-loaded preview (`splitApprovable`'s `knownPreview`, no fetch of its own); the rest open `PendingReviewDialog` grouped by reason, each record sent with its own fingerprint, and every sweep reports a per-record result row (a refused revert included) — a record the sweep found needing an acknowledgement is reported AND handed to that grouped dialog (approve or dismiss with the acknowledgement). A batch (the sweep, a dialog group) HOLDS the source revisions its own writes bump (`holdRevisions`, released in `afterMutation`): N writes cost N verb requests, ONE re-list and at most one re-preview per card still listed — never a re-list plus every visible card's re-preview per write. A `changed` answer (`PENDING_STATE_CHANGED` / `PENDING_GENERATION_CHANGED`) is not final: the dialog fetches ONE fresh preview for that record (per-record sequence, liveness cleared on unmount only) and waits for a new click — never a replay. In the panel that ONE fetch is the panel's `refetch`: it waits for the re-list, the record's card holds meanwhile and adopts the answer under its final key (`takeRefetch`), so the card sends nothing of its own; a direct (dialog-less) refusal bumps only that card's preview nonce. A confirmed absence with a saved baseline is named in the preview body (`acceptsAbsence`). The orphan probe runs on mount, Refresh and Repair only — a source revision re-reads the plain list. Source inventory is separate from content, completed siblings are cached, truncation is shown, and Git errors do not hide other sources. Review reads a bounded pending preview/fingerprint with typed current/baseline/index states; ack-required state opens an explicit confirmation. Actual WRITE access gates card, compact, bulk and repair controls; historical cards remain read-only. Orphan ids arrive with the same pending listing, so Repair remains orphan-only and re-authorized server-side. Changes exposes Load more and incomplete inventory state. Repair processes batches sequentially with progress and Stop after the current batch; partial pages pause at their cursor for explicit Continue available/Retry. List and orphan epochs are independent; classification survives a plain relist only for matching record generations. FileEditor opens the shared review dialog for the exact visible URI. Returned generation conflicts appear in the existing Changes row status before preview succeeds. Git hunk rows retain geometry during same-context permission refresh while actions remain disabled until permission and diff settle.
 
 - `InlineUploader` — the Upload tab (folder pick, new folder, drop zone). The two modals it once sat beside (`EditFileModal`, `UploadFileModal`) were deleted 2026-09-04: nothing had mounted either since the repository's baseline, so the settling-sandpiper M9 reconcile tails had been fixed on dead code while the live in-place Edit still called the upsert-only `refresh`. Those tails are store actions now (`saveFileInPlace` / `markFileDeleted`, `../store/README.md`) that `FileEditor` calls.
 - `GitControlPanel`, `StackedSections` (+ pure `stackedSectionsLayout.ts`), `GitCommitGraph` (+ pure `gitGraphLayout.ts`/`gitGraphPaging.ts`/`gitGraphItems.ts` — the item model: expandable rows, the outgoing divider, ref-chip/dot classing, the branch-bar ahead/behind chips), `GitDiffView` + `GitFileDiff` + `GitCommitChangesView` (re-exported; + pure `gitDiffExpand.ts`/`gitDiffPatch.ts`/`gitFileDiffMode.ts`), `GitStatusBadge`, `DiffCountBadge` — the Git Control surface: the sidebar pane-stack panel, the in-panel virtualized commit graph with commit drill-in + outgoing markers, the side-by-side diff view (single + multi-file stacked tab), the per-file tree badge. The owning narrative (sections, paging/live-refresh, drill-in, outgoing, caps, write gating) is the package-root README "Git Control panel" section — this bullet only anchors the files.
@@ -39,7 +39,7 @@ Re-exported from `app/filesystem/ui/index.ts`:
 - `PolicyEditor` — compact admin-style permissions editor for the source-config panel. Renders the persisted JSON tree (`default`, `byRole`, `byUser`, `byAgent`, `paths[]`) with tri-state R/W/X pill badges (allow / deny / inherit cycle), per-role/user/agent override rows (with `+ Add` input + trash), and path rules with clickable role chips + per-rule agent chips (`$self/agentId`, inline-add). `OVR` toggles the rule's `override` flag. Adding a rule **prepends** it (visible at the top of long policy sets; first-match-wins means the fresh rule also takes precedence). Two modes: `edit` (Save button visible when dirty) and `view` (read-only chat-config render). It is wired into `SourcesPanel`, laid out admin-style, and carries the By Role / By User / By Agent sections. Save threads through `handlePolicySave` → `updateSourceConfig` without disturbing the user's pending sync/credential edits.
 - `SourcesPanel` "Discoverable" section — lives INSIDE the Vector Health expandable, alongside a `mount.mts` explainer card. Suggestions arrive from `GET /sources/discoverable` and use the shared `dimmedSourceTone('unattached')` util. The icon name (`AppWindow`, `GitBranch`, `FolderTree`, …) resolves through the shared `resolveLucideIcon` helper (same `ICON_MAP` as the workspace dock-left). Click pre-fills the add-source form with `{ key, path, kind, hostRoot? }` from the suggestion, plus the suggestion's optional `suggestedAccess` (read/write/exec) which overrides the connector-kind default, and — for `seed:'discoverable'` package declarations (e.g. the admin app zone, suggestion id `discover:decl:app`) — the **declared `description`** prefills the add form's description field. The **Full Host** suggestion (native/non-Docker only — `/` is the readable host root; in Docker the host must first be bound via `pnpm neuralis:mount add /`) ships `suggestedAccess: { read:true, write:false, exec:false }` so the whole-host root attaches **read-only by default** — the owner widens it (or narrows the uri-policy) in the form before saving. A host source is readable from the container shell, but host-native binaries still won't execute under the container runtime (a host PTY broker is a separate, future capability).
 - `SourcesPanel` row actions say what they do: **Rescan changes** (the `reindex` route without `force` — changed files are embedded again, unchanged ones keep their vectors), **Re-embed…** (`ReembedDialog` — every file of the source with the active model, estimate first), **Embed pending…** (`ReembedDialog kind="pending"`; it and **Re-embed…** are disabled while the row's live `embedding_enabled` says off), **Forget sync state** (the `reset` route — the next sync compares every file again; deletes no file and no vector). A started re-embed is followed by the same job poll + count refresh as a rescan (`followReindex`); an embedding pass that ends `paused` (terminal, not failed) shows "Embedding paused: <reason>" with **Resume** (the same owed-only apply). The Modify-source body states `binarySkipLine` ("N binary files not indexed" — the last count a pass measured) and `embeddingLine` beside `mediaSkipLine`: off — the live `embedding_enabled`, never the last pass — reads neutral ("Semantic embedding off — text and field search only"); the last pass's other reasons read amber ("Semantic embedding pending: <reasons>").
-- `SourcesPanel` row is **name-first** (the redesign for the always-narrow widget). The source name is the dominant element (`flex-1`, larger/bold); the kind icon uses the SAME resolved icon set as the file tree (`resolveIconWithFallback` over the connector-manifest `kind_icon`/`meta.icon`) and is **coloured by `getSourceVisualTone`** — so the icon tone IS the sync/live signal, matching the tree (the old `Healthy/Idle/Error` status text + `statusTone` are gone). The per-row **trust badge** (`first-party`/…) and the **scope badge** (`project`/`user`/`agent` — already a tab filter above) are removed; only `observed`, `orphan`, `unsaved`, and the enabled toggle remain inline. Rows are **grouped by `origin_package`** — the **declaring package id** the server resolves per source (the CONTRACT-BACKED `PackageSourceDeclaration` owner, returned on each `SourceRuntimeSummary` / `s.origin_package`), one group **per package**: each real `@neuralis/*` (or any other) package sorts **alphabetically** and user-added mounts collapse into a single **`Mounted (user-added)`** group that sorts **LAST** (`sourceOriginGroup` / `MOUNTED_GROUP`). The small left-indented group header **replaces** the per-row trust/`first-party` badge. The old client-side heuristic that inferred the owner from the connector kind's npm scope (`sourceOriginLabel`) is **gone** — attribution is now resolved server-side from the declarations (`matchDeclaredSource`, slug + resolved-root for rooted kinds; kind-only for rootless sandbox kinds), so a user mount named `app` that is NOT rooted at the platform app zone is NOT attributed to admin — the grouping is **unspoofable**.
+- `SourcesPanel` row is **name-first** (the redesign for the always-narrow widget). The source name stays left-aligned and is the dominant element (`flex-1`, larger/bold); the kind icon uses the SAME resolved icon set as the file tree (`resolveIconWithFallback` over the connector-manifest `kind_icon`/`meta.icon`) and is **coloured by `getSourceVisualTone`** — so the icon tone IS the sync/live signal, matching the tree (the old `Healthy/Idle/Error` status text + `statusTone` are gone). The per-row **trust badge** (`first-party`/…) and the **scope badge** (`project`/`user`/`agent` — already a tab filter above) are removed; only `observed`, `orphan`, `unsaved`, and the enabled toggle remain inline. Rows are **grouped by `origin_package`** — the **declaring package id** the server resolves per source (the CONTRACT-BACKED `PackageSourceDeclaration` owner, returned on each `SourceRuntimeSummary` / `s.origin_package`), one group **per package**: each real `@neuralis/*` (or any other) package sorts **alphabetically** and user-added mounts collapse into a single **`Mounted (user-added)`** group that sorts **LAST** (`sourceOriginGroup` / `MOUNTED_GROUP`). The small left-indented group header **replaces** the per-row trust/`first-party` badge. The old client-side heuristic that inferred the owner from the connector kind's npm scope (`sourceOriginLabel`) is **gone** — attribution is now resolved server-side from the declarations (`matchDeclaredSource`, slug + resolved-root for rooted kinds; kind-only for rootless sandbox kinds), so a user mount named `app` that is NOT rooted at the platform app zone is NOT attributed to admin — the grouping is **unspoofable**.
 - `SourcesPanel` source body: when a row is expanded it renders at **full height** (no `max-h` clamp) so every Path Rule / uri-policy is visible and the outer panel scrolls — the closed state keeps the collapse animation. The Sync sub-section shows a per-trigger explainer (Manual = only the Sync button; Auto = file-watch + reconcile; Scheduled = interval) and clarifies the "Always active" pin. Disabling sync (unchecking "Enable sync" + Save) sends `clearSync: true` — an omitted `sync` means "no change" server-side, so without the flag the disable would silently revert.
 - `SourcesPanel` per-source counts are **lazy** — the exact `connector` / `indexed` / `unindexed` stats row is fetched ONLY when its row is opened (`toggleSource` → `fetchSourceCounts` → a list scoped to `<source>://` with `include_counts`, so `computeSourcesRegistry` walks that ONE source), cached in `countsBySource`, and shown behind a "Loading counts…" placeholder. Panel-open itself does a **count-FREE** `refresh()` (no `withCounts`) — that still populates `sourceSummaries` (`s.sources`) for source discovery (observed-only sources, project scope) + per-row connector liveness dim, but fires **zero** project-wide count walks. There is deliberately no eager `refresh({withCounts:true})` on open — that, together with the Vector Health walk below, is what used to make opening one panel slow everything. Counted refreshes are narrowed to the operations that actually MOVE a number: sync, reindex, and a config save that changed the sync FILTER set (`syncFilterChanged` — exclude/include/`maxScanFiles`/a cleared sync block, which `connector.count()` applies, so the on-disk total shifts at once). A permissions save, a delete and an add refresh count-FREE: the indexed count is a project-scoped `countByFilter` with no per-caller policy input, the on-disk count is physical truth, a deleted row is gone and a brand-new row's numbers are one expand away. Every counted path also evicts that source's cached counts (`clearCachedCounts`) so the fresh summary is what renders — the lazy cache used to shadow it indefinitely after an exclude edit. `pollSyncJob` (1.5 s × `MAX_POLLS` 2400 = a sixty-minute ceiling) checks a `mountedRef` each turn and returns the moment the panel unmounts; the ref is cleared on UNMOUNT ONLY, never in a dependency-change cleanup, so a live poll is never dropped while the panel is still there. And EVERY hook in `SourcesPanel` sits above its `if (!open) return null` guard: two `useCallback`s used to live below it, so the component rendered a different number of hooks open than closed — React refuses that on one instance, and only the parent's mount gate carrying the same `workspacePanels.sources` flag kept it from ever firing.
 - `useFilesystemSSE` `sync:completed`: the handler is matched **before** the `if (!uri) return` guard — the event carries `source` (the slug), NOT a file `uri`. It runs the authoritative `reconcileSourceFolders` over that source's VISIBLE folders (a sync can have removed files), skips the pass entirely when every change count on the payload is zero (a missing count is unknown and still re-lists), and falls back to `refreshTree` only when no source is present. That pass rides the ONE per-source reconcile schedule shared with external-change events (a trailing quiet window with a max-wait), so a burst of changes becomes one pass. Owner: `app/filesystem/hooks/README.md`.
@@ -53,13 +53,13 @@ Re-exported from `app/filesystem/ui/index.ts`:
 
 - `SourceDeleteConfirm` — inline rose-tinted popover under the row (no modal, matches the panel's "no overlay" pattern). Headline + one-line reminder that the host folder is not touched + `[ ] Purge vector index entries (~N point(s))` checkbox (default OFF — conservative) + Docker-bind-mount warning ribbon when `connection.config.hostRoot` is set, telling the user to run `neuralis mount remove <slug>` before restarting the container. On confirm, `SourcesPanel.handleDelete` calls `deleteSource({ purgeVectors })` and surfaces a transient `successMsg` ("Deleted "<source>" (vectors purged: N)").
 - **`SkillLauncher` coverage** (`@neuralis/package-system/client`, additive "+" launchers) — every filesystem function the LLM can drive has a visible composer-prefill trace. Clicking a launcher PREFILLS the chat composer with the skill (+ scripts) like a `/` slash pick; it never sends/streams. **No launcher states a feature list**: visibility is DERIVED from the host's per-caller skill catalog, so it cannot drift from each skill's own `SKILL.md` `requiredFeatures` and an unresolved catalog renders nothing (the gate named per row below is the SKILL's, documented here, not repeated in the JSX). `packageId` is the REGISTRY id (`@neuralis/brain-core`), matched as an exact pair with the skill id. The launchers resolve the `WorkspaceHostPort` from the `WorkspaceHostPortProvider` mounted once in `host/installFilesystemHostComponents.tsx` — without it they render `null` silently. Current placements:
-  - `Toolbar` — `sync` (`drive.sync`, icon-`brain`, script-less) next to the Sources panel toggle, and `manage-files` (`drive.write`; `scripts: mkdir, copy, modify, search`) as the general file-ops handoff. The tree's CONTEXT MENU deliberately carries none: it is a keyboard-navigable click-to-act list with one uniform item model, and a composer-prefill affordance would need a bespoke item kind there.
-  - `SourcesPanel` header — `manage-sources` (`drive.read`, attached-left to the `+ Source` button; `scripts: sync, reindex, set-enabled`).
-  - `SourcesPanel` per-source **Permissions** header — `manage-uri-policy` (`drive.policy` — no grant below the `admin` tier, grantable to any custom role; `scripts: show-uri, set-uri, manifests`) hands the URI-policy / path-permission edit for that source to the agent, alongside the `PolicyEditor`.
+  - `Toolbar` — `sync` (`drive.sync`, icon-`brain`, script-less) next to the Sources panel toggle, and `manage-files` (`drive.write`; `scripts: mkdir, copy, modify`) as the general file-ops handoff. The tree's CONTEXT MENU deliberately carries none: it is a keyboard-navigable click-to-act list with one uniform item model, and a composer-prefill affordance would need a bespoke item kind there.
+  - `SourcesPanel` header — `manage-sources` (`drive.read`, attached-left to the `+ Source` button).
+  - `SourcesPanel` per-source **Permissions** header — `manage-uri-policy` (`drive.policy` — no grant below the `admin` tier, grantable to any custom role) hands the URI-policy / path-permission edit for that source to the agent, alongside the `PolicyEditor`.
   - `FileTree` empty-state — `manage-files` (`drive.write`, label; `scripts: upload, modify`) to populate a source.
-  - `GitControlPanel` header — `git` (`drive.read`; `scripts: git.sh`) next to the refresh button. The `git` skill drives the SAME `/git/*` routes this panel does — its own SKILL.md says so — and the panel shipped with no way to reach it until 2026-07-28.
-  - `PendingChangesPanel` toolbar — `manage-files` (`drive.write`; `scripts: pending, approve`) for bulk review; the per-row approve/revert buttons stay the primary path.
-  - `VectorHealthPanel` actions row — `manage-sources` (`drive.read`; `scripts: sync-status, reindex`). The index is per-SOURCE, so the agent-side equivalent of scan/repair is a source reindex plus a sync-status readout.
+  - `GitControlPanel` header — `git` (`drive.read`) next to the refresh button. The `git` skill drives the SAME `/git/*` routes this panel does — its own SKILL.md says so — and the panel shipped with no way to reach it until 2026-07-28.
+  - `PendingChangesPanel` toolbar — `manage-files` (`drive.write`) for bulk review; the per-row approve/revert buttons stay the primary path.
+  - `VectorHealthPanel` actions row — `manage-sources` (`drive.read`). The index is per-SOURCE, so the agent-side equivalent of scan/repair is a source reindex plus a sync-status readout.
   - `PackagesPanel` header — `create-package` (label, script-less) hands the whole authoring flow (scaffold, manifest, tools, surfaces, connectors, build — including the WASM pipeline) to the agent; additive to the per-row `Build` button. This is the ONE launcher that narrows further, with `alsoRequires={["packages.author"]}`, even though the SKILL ships ungated (so it stays importable): it scaffolds into `packages://`, which needs write + install/build capability the default `member` role does not hold, so showing it to a caller whose first action would be denied is worse UX than hiding it. `alsoRequires` can only ever hide a launcher, never reveal one, so this cannot become a disclosure. Deliberate — do not "align" it with the skill frontmatter.
 
 ## How it plugs into the package-system kernel

package/app/filesystem/ui/ReembedDialog.tsx

@@ -18,6 +18,7 @@ import { useEffect, useState } from 'react';
 import { createPortal } from 'react-dom';
 import { Loader2, RefreshCcw, X } from 'lucide-react';
 import { estimateReembed, startReembed, type ReembedEstimate, type ReembedKind } from '../api';
+import { useFilesystemStore } from '../store/filesystemStore';
 
 export type ReembedTarget = {
   source: string;
@@ -58,6 +59,7 @@ export function ReembedDialog({
   /** Called after a job was queued — the caller follows it however it follows sync jobs. */
   onStarted?: () => void;
 }) {
+  const client = useFilesystemStore((s) => s.client);
   const [estimate, setEstimate] = useState<ReembedEstimate | null>(null);
   const [estimating, setEstimating] = useState(true);
   const [starting, setStarting] = useState(false);
@@ -75,7 +77,7 @@ export function ReembedDialog({
   useEffect(() => {
     let live = true;
     setEstimating(true);
-    estimateReembed(scope, kind)
+    estimateReembed(scope, kind, client)
       .then((result) => {
         if (live) setEstimate(result);
       })
@@ -108,7 +110,7 @@ export function ReembedDialog({
     setStarting(true);
     setError(null);
     try {
-      const started = await startReembed(scope, kind);
+      const started = await startReembed(scope, kind, client);
       if (!started.job) {
         // Nothing readable in scope — the route queued nothing. Say so.
         setNothingToDo(true);

package/app/filesystem/ui/SourcesPanel.tsx

@@ -470,6 +470,7 @@ const textareaCls = cn(
 // ---------------------------------------------------------------------------
 
 export function SourcesPanel(props: Props) {
+  const client = useFilesystemStore((s) => s.client);
   const { agentId, projectId, isDocker } = props;
   const open = useFilesystemStore((s) => s.workspacePanels.sources);
   const setWorkspacePanelOpen = useFilesystemStore((s) => s.setWorkspacePanelOpen);
@@ -577,7 +578,7 @@ export function SourcesPanel(props: Props) {
   // schema-driven picker (replacing the old hardcoded KIND_META).
   useEffect(() => {
     let cancelled = false;
-    listSourceKinds()
+    listSourceKinds(client)
       .then((res) => {
         if (cancelled) return;
         setKinds(res.kinds ?? []);
@@ -704,8 +705,8 @@ export function SourcesPanel(props: Props) {
           agentId,
           projectId,
           scope: activeScope,
-        }),
-        listDiscoverableSources({ agentId, projectId })
+        }, client),
+        listDiscoverableSources({ agentId, projectId }, client)
           .catch(() => ({ suggestions: [] as DiscoverableSourceSuggestion[] })),
       ]);
       setConfigs(next);
@@ -746,7 +747,7 @@ export function SourcesPanel(props: Props) {
     });
     if (alreadyLoading) return;
     try {
-      const info = await fetchSourceCounts(agentId, projectId ?? undefined, source);
+      const info = await fetchSourceCounts(agentId, projectId ?? undefined, source, client);
       if (info) setCountsBySource((prev) => ({ ...prev, [source]: info }));
     } catch {
       // Count failure is non-fatal — the row still works, the stats row just stays blank.
@@ -793,7 +794,7 @@ export function SourcesPanel(props: Props) {
   useEffect(() => {
     if (!showAddForm || !isDocker || !canMount) return;
     setDockerMountsLoading(true);
-    browseDirectories({ path: '/mounts', agentId, ...(projectId ? { projectId } : {}) })
+    browseDirectories({ path: '/mounts', agentId, ...(projectId ? { projectId } : {}) }, client)
       .then((result) => {
         // Filter out volumes already configured as sources
         const configuredSources = new Set(configs.map((c) => c.source));
@@ -905,7 +906,7 @@ export function SourcesPanel(props: Props) {
         agentId,
         ...(projectId ? { projectId } : {}),
         config: { ...payload, ...(clearSync ? { clearSync: true } : {}) },
-      });
+      }, client);
       setConfigs((s) => s.map((e) => (e.source === updated.source ? updated : e)));
       setDrafts((s) => ({ ...s, [updated.source]: buildDraft(updated) }));
       // Counted refresh ONLY when the save moved the sync FILTER set — that is
@@ -943,7 +944,7 @@ export function SourcesPanel(props: Props) {
           agentId,
           ...(projectId ? { projectId } : {}),
           config: { ...currentDraft, permissions: nextPerms },
-        });
+        }, client);
         setConfigs((s) => s.map((e) => (e.source === updated.source ? updated : e)));
         setDrafts((s) => ({ ...s, [updated.source]: buildDraft(updated) }));
         // A permissions edit moves no number: the indexed count is a
@@ -977,7 +978,7 @@ export function SourcesPanel(props: Props) {
       // is cleared on UNMOUNT ONLY (never in a dependency-change cleanup), so a
       // live poll is never dropped while the panel is still mounted.
       if (!mountedRef.current) return null;
-      const status = await getSyncStatus({ agentId, ...(projectId ? { projectId } : {}), source });
+      const status = await getSyncStatus({ agentId, ...(projectId ? { projectId } : {}), source }, client);
       const job = status.job;
       if (!job) return null;
       if (job.status === 'pending' || job.status === 'running') continue;
@@ -1005,7 +1006,7 @@ export function SourcesPanel(props: Props) {
     setSyncingSource(source);
     setError(null);
     try {
-      await triggerSourceSync({ agentId, ...(projectId ? { projectId } : {}), source });
+      await triggerSourceSync({ agentId, ...(projectId ? { projectId } : {}), source }, client);
       await pollSyncJob(source);
       await load();
       await refresh({ agentId, projectId, withCounts: true });
@@ -1019,7 +1020,7 @@ export function SourcesPanel(props: Props) {
 
   const handleCancelSync = async (source?: string) => {
     try {
-      await cancelSync({ agentId, ...(projectId ? { projectId } : {}), ...(source ? { source } : {}) });
+      await cancelSync({ agentId, ...(projectId ? { projectId } : {}), ...(source ? { source } : {}) }, client);
       // The polling loop in handleSync/handleReindex observes the cancelled
       // status and clears the spinner; clear eagerly for instant feedback.
       setSyncingSource(null);
@@ -1058,7 +1059,7 @@ export function SourcesPanel(props: Props) {
   const handleResumeEmbedding = (source: string) =>
     followReindex(
       source,
-      () => startReembed({ agentId, ...(projectId ? { projectId } : {}), source }, 'pending'),
+      () => startReembed({ agentId, ...(projectId ? { projectId } : {}), source }, 'pending', client),
       'Embedding failed',
     );
 
@@ -1066,7 +1067,7 @@ export function SourcesPanel(props: Props) {
   const handleReindex = (source: string) =>
     followReindex(
       source,
-      () => reindexSource({ agentId, ...(projectId ? { projectId } : {}), source }),
+      () => reindexSource({ agentId, ...(projectId ? { projectId } : {}), source }, client),
       'Rescan failed',
     );
 
@@ -1076,7 +1077,7 @@ export function SourcesPanel(props: Props) {
     setPurgeBusy(true);
     setError(null);
     try {
-      const counts = await purgeSourceIndex({ agentId, ...(projectId ? { projectId } : {}), source, selector, mode, obsoleteOnly: purgeObsoleteOnly });
+      const counts = await purgeSourceIndex({ agentId, ...(projectId ? { projectId } : {}), source, selector, mode, obsoleteOnly: purgeObsoleteOnly }, client);
       if (epoch !== purgeEpoch.current) return;
       if (mode === 'estimate') setPurgeCounts(counts);
       else { setPurgeFor(null); setPurgeCounts(null); clearCachedCounts(source); await load(); await refresh({ agentId, projectId, withCounts: true }); }
@@ -1088,7 +1089,7 @@ export function SourcesPanel(props: Props) {
     setResettingSource(source);
     setError(null);
     try {
-      await resetSync({ agentId, ...(projectId ? { projectId } : {}), source });
+      await resetSync({ agentId, ...(projectId ? { projectId } : {}), source }, client);
       await load();
     } catch (err) {
       setError(err instanceof Error ? err.message : 'Reset failed');
@@ -1107,7 +1108,7 @@ export function SourcesPanel(props: Props) {
     setTogglingEnabledSource(source);
     setError(null);
     try {
-      await setSourceEnabled({ agentId, ...(projectId ? { projectId } : {}), source, enabled: next });
+      await setSourceEnabled({ agentId, ...(projectId ? { projectId } : {}), source, enabled: next }, client);
       await load();
     } catch (err) {
       setError(err instanceof Error ? err.message : 'Toggle failed');
@@ -1125,7 +1126,7 @@ export function SourcesPanel(props: Props) {
         ...(projectId ? { projectId } : {}),
         source,
         ...(opts.purgeVectors ? { purgeVectors: true } : {}),
-      });
+      }, client);
       await load();
       // The deleted row is gone; no surviving source's count moved, so the
       // refresh runs count-free. `clearCachedCounts` still drops the row's own
@@ -1151,7 +1152,7 @@ export function SourcesPanel(props: Props) {
     setBrowseLoading(true);
     setBrowseError(null);
     try {
-      const result = await browseDirectories({ path, agentId, ...(projectId ? { projectId } : {}) });
+      const result = await browseDirectories({ path, agentId, ...(projectId ? { projectId } : {}) }, client);
       setBrowseEntries(result.entries);
       setBrowsePath(path);
     } catch {
@@ -1212,7 +1213,7 @@ export function SourcesPanel(props: Props) {
         ...(isOwnerEffective && addKind === 'local' && addDraft.recognizesPackages
           ? { recognizesPackages: true }
           : {}),
-      });
+      }, client);
       setShowAddForm(false);
       {
         const reset = buildAddDraft(selectedKind, sourceKeyIds);
@@ -1260,7 +1261,6 @@ export function SourcesPanel(props: Props) {
               attached="left"
               skill="manage-sources"
               packageId="@neuralis/brain-core"
-              scripts={["scripts/sync.sh", "scripts/reindex.sh", "scripts/set-enabled.sh"]}
               label="Manage sources with the agent"
             />
           </div>
@@ -1672,13 +1672,11 @@ export function SourcesPanel(props: Props) {
 
           return (
             <div key={fileKey(sourceRootUri(config.source))} className="rounded-sm">
-              {/* Accordion header */}
-              <button
-                type="button"
-                onClick={() => toggleSource(config.source)}
-                title={disconnected ? sourceLiveReasonLabel(config.live_reason) : undefined}
-                className="w-full flex items-center gap-2 py-2 text-left group hover:bg-white/[0.02] rounded-md px-1 transition"
-              >
+              {/* Accordion header: selection and enabled actions are siblings. */}
+              <div className="w-full flex items-center gap-2 py-2 text-left group hover:bg-white/[0.02] rounded-md px-1 transition">
+                <button type="button" onClick={() => toggleSource(config.source)} aria-expanded={isOpen}
+                  title={disconnected ? sourceLiveReasonLabel(config.live_reason) : undefined}
+                  className="min-w-0 flex-1 flex items-center gap-2 text-left">
                 {/* Git indicator (G2.1) — a GitBranch overlay on a git-repo
                     source's icon, ORTHOGONAL to the sync tone (visualTone still
                     owns the icon colour). */}
@@ -1713,6 +1711,7 @@ export function SourcesPanel(props: Props) {
                 {dirty && (
                   <span className="shrink-0 rounded px-1 py-0.5 text-[8px] font-medium text-amber-300/80 bg-amber-500/10">unsaved</span>
                 )}
+                </button>
                 {/* W3K — enabled toggle (per scope, per source). Machine sources also offer Auto. */}
                 {(() => {
                   const enabled = config.enabled ?? true;
@@ -1763,7 +1762,7 @@ export function SourcesPanel(props: Props) {
                   {describeConn(config, meta)}
                 </span>
                 <ChevronDown className={cn('h-3 w-3 text-white/25 shrink-0 transition-transform', isOpen && 'rotate-180')} />
-              </button>
+              </div>
 
               {/* Expanded body — when open it expands to full height (no clamp)
                   so every Path Rule / uri-policy is visible; the outer panel
@@ -1902,7 +1901,6 @@ export function SourcesPanel(props: Props) {
                         size="sm"
                         skill="manage-uri-policy"
                         packageId="@neuralis/brain-core"
-                        scripts={["scripts/show-uri.sh", "scripts/set-uri.sh", "scripts/manifests.sh"]}
                         label={`Edit URI policy for "${config.source}" with the agent`}
                         icon="shield"
                       />

package/app/filesystem/ui/Toolbar.tsx

@@ -20,6 +20,7 @@ export function Toolbar(props: { agentId: string; onOpenProjectFiles: () => void
   const activeWorkspaceTab = useFilesystemStore((s) => s.activeWorkspaceTab);
   // The server count of the caller's visible pending reviews (`refreshPendingCount`),
   // never the client set of loaded folders' rows.
+  const pendingCountState = useFilesystemStore((s) => s.pendingCountState);
   const pendingCount = useFilesystemStore((s) => s.pendingCount);
 
   return (
@@ -112,7 +113,7 @@ export function Toolbar(props: { agentId: string; onOpenProjectFiles: () => void
           size="sm"
           skill="manage-files"
           packageId="@neuralis/brain-core"
-          scripts={["scripts/mkdir.sh", "scripts/copy.sh", "scripts/modify.sh", "scripts/search.sh"]}
+          scripts={["scripts/mkdir.sh", "scripts/copy.sh", "scripts/modify.sh"]}
           label="Create, copy, edit or search files with the agent"
           icon="Folder"
         />
@@ -133,7 +134,7 @@ export function Toolbar(props: { agentId: string; onOpenProjectFiles: () => void
 
         <button
           className={`relative p-1.5 rounded-lg transition-colors ${workspacePanels.pending && activeWorkspaceTab === 'pending' ? 'bg-amber-500/15 text-amber-300' : 'text-white/50 hover:bg-white/5 hover:text-amber-200'}`}
-          title={pendingCount > 0 ? `Pending changes — ${pendingCount} to review` : 'Pending changes — review, approve & revert'}
+          title={pendingCountState === 'stale' ? `Pending changes — count unavailable${pendingCount > 0 ? ` (last count ${pendingCount})` : ''}` : pendingCountState === 'partial' ? `Pending changes — ${pendingCount}+ (incomplete) to review` : pendingCount > 0 ? `Pending changes — ${pendingCount} to review` : 'Pending changes — review, approve & revert'}
           onClick={() => {
             if (workspacePanels.pending && activeWorkspaceTab === 'pending') {
               setWorkspacePanelOpen('pending', false);
@@ -143,9 +144,9 @@ export function Toolbar(props: { agentId: string; onOpenProjectFiles: () => void
           }}
         >
           <FileDiff className="w-4 h-4" />
-          {pendingCount > 0 ? (
+          {pendingCount > 0 || pendingCountState !== 'exact' ? (
             <span data-testid="pending-count-badge" className="absolute -top-1 -right-1 min-w-[14px] rounded-full px-1 text-center text-[9px] leading-[14px] font-semibold bg-amber-500/15 text-amber-300">
-              {pendingCount >= 1000 ? '1000+' : pendingCount}
+              {pendingCount > 999 ? '1000+' : pendingCount}{pendingCountState === 'partial' && pendingCount <= 999 ? '+' : pendingCountState === 'stale' ? '?' : ''}
             </span>
           ) : null}
         </button>

package/app/filesystem/ui/VectorHealthPanel.tsx

@@ -7,6 +7,7 @@ import { hasFeature } from '@neuralis/package-system/access';
 import { useFilesystemHost } from '../FilesystemHost';
 import { cn } from '../lib/cn';
 import { checkVectorHealth, scanVectorHealth, runHealthAction, getSourcesHealth } from '../api';
+import { useFilesystemStore } from '../store/filesystemStore';
 
 type Props = {
   agentId: string;
@@ -73,6 +74,7 @@ const ACTION_COPY: Record<ActionKind, { label: string; explainer: string; toolti
 };
 
 export function VectorHealthPanel({ agentId, projectId }: Props) {
+  const client = useFilesystemStore((s) => s.client);
   const host = useFilesystemHost();
   // A mirror only — the server's `drive.write` escalation is the gate.
   const canWrite = hasFeature({ grantedFeatures: [...(host.grantedFeatures ?? [])] }, 'drive.write');
@@ -97,9 +99,17 @@ export function VectorHealthPanel({ agentId, projectId }: Props) {
    *  Cleared automatically after 3s. Skipped when `dryRun === true` since
    *  preview-only doesn't need a guard. */
   const [confirmingAction, setConfirmingAction] = useState<ActionKind | null>(null);
+  const epoch = useRef(0);
+  const reportSeq = useRef(0);
+  const scanSeq = useRef(0);
+  const stop = useRef(false);
+  const pendingCursor = useRef<string | undefined>(undefined);
+  const [pendingPaused, setPendingPaused] = useState(false);
+  useEffect(() => { pendingCursor.current = undefined; setPendingPaused(false); }, [dryRun, retentionHours]);
   const confirmTimerRef = useRef<ReturnType<typeof setTimeout> | null>(null);
 
   const fetchReport = useCallback(async () => {
+    const mine = epoch.current; const request = ++reportSeq.current;
     setLoading(true);
     setError(null);
     try {
@@ -108,8 +118,8 @@ export function VectorHealthPanel({ agentId, projectId }: Props) {
       // table so it surfaces real "when was this source last synced"
       // info instead of being a count-only view.
       const [data, sourcesHealth] = await Promise.all([
-        checkVectorHealth({ agentId, ...(projectId ? { projectId } : {}) }),
-        getSourcesHealth({ agentId, ...(projectId ? { projectId } : {}) })
+        checkVectorHealth({ agentId, ...(projectId ? { projectId } : {}) }, client),
+        getSourcesHealth({ agentId, ...(projectId ? { projectId } : {}) }, client)
           .catch(() => [] as Array<{ source: string; last_sync?: string; sync_status: string }>),
       ]);
       const lastSyncBySource = new Map<string, { last_sync?: string; sync_status: string }>();
@@ -126,26 +136,29 @@ export function VectorHealthPanel({ agentId, projectId }: Props) {
           return meta ? { ...row, ...meta } : row;
         });
       }
+      if (mine !== epoch.current || request !== reportSeq.current) return;
       setReport(enriched);
     } catch (err) {
-      setError(err instanceof Error ? err.message : 'Failed to fetch health report');
+      if (mine === epoch.current && request === reportSeq.current) setError(err instanceof Error ? err.message : 'Failed to fetch health report');
     } finally {
-      setLoading(false);
+      if (mine === epoch.current && request === reportSeq.current) setLoading(false);
     }
-  }, [agentId, projectId]);
+  }, [client, agentId, projectId]);
 
   const runScan = useCallback(async () => {
+    const mine = epoch.current; const request = ++scanSeq.current;
     setScanLoading(true);
     setError(null);
     try {
-      const result = await scanVectorHealth({ agentId, ...(projectId ? { projectId } : {}) });
+      const result = await scanVectorHealth({ agentId, ...(projectId ? { projectId } : {}) }, client);
+      if (mine !== epoch.current || request !== scanSeq.current) return;
       setScan({ orphanChunkCount: result.orphanChunkCount ?? 0, duplicateGroups: result.duplicateGroups ?? 0 });
     } catch (err) {
-      setError(err instanceof Error ? err.message : 'Scan failed');
+      if (mine === epoch.current && request === scanSeq.current) setError(err instanceof Error ? err.message : 'Scan failed');
     } finally {
-      setScanLoading(false);
+      if (mine === epoch.current && request === scanSeq.current) setScanLoading(false);
     }
-  }, [agentId, projectId]);
+  }, [client, agentId, projectId]);
 
   const runAction = useCallback(async (action: ActionKind) => {
     // Two-click confirm for destructive actions when not in dry-run mode.
@@ -160,6 +173,7 @@ export function VectorHealthPanel({ agentId, projectId }: Props) {
       confirmTimerRef.current = null;
     }
     setConfirmingAction(null);
+    const mine = epoch.current; stop.current = false;
     setActionLoading(true);
     setActionResult(null);
     setLastActionKind(action);
@@ -168,8 +182,22 @@ export function VectorHealthPanel({ agentId, projectId }: Props) {
     // we're actually deleting something (`dryRun=false`).
     setPrevReport(!dryRun ? report : null);
     try {
-      const result = await runHealthAction({ agentId, ...(projectId ? { projectId } : {}), action, dryRun, retentionHours });
-      setActionResult(result);
+      let cursor = action === 'repair-pending' ? pendingCursor.current : undefined; setPendingPaused(false);
+      const totals: Record<string, number> = {};
+      do {
+        const result = await runHealthAction({ agentId, ...(projectId ? { projectId } : {}), action, dryRun, retentionHours, ...(cursor ? { cursor } : {}) }, client);
+        if (mine !== epoch.current) return;
+        for (const key of ['scannedVisible', 'orphaned', 'attempted', 'discarded', 'refused', 'failed', 'legacyUnknownDraft']) {
+          if (typeof result[key] === 'number') totals[key] = (totals[key] ?? 0) + result[key];
+        }
+        setActionResult({ ...result, ...totals });
+        cursor = action === 'repair-pending' && !result.restartRequired && typeof result.nextCursor === 'string' ? result.nextCursor : undefined;
+        if (action === 'repair-pending') pendingCursor.current = cursor;
+        if (result.partial === true) { setPendingPaused(true); setError('Repair paused; part of the inventory or orphan checks are unavailable.'); break; }
+        if (result.restartRequired) { pendingCursor.current = undefined; setPendingPaused(true); setError('Changes moved. Refresh before continuing repair.'); }
+        if (typeof result.failed === 'number' && result.failed > 0) { cursor = undefined; setPendingPaused(true); setError('Repair paused after a failed change. Refresh before continuing.'); }
+      } while (cursor && !stop.current);
+      if (cursor) setPendingPaused(true);
       if (!dryRun) {
         void fetchReport();
         // A destructive action changes orphan/dup counts — refresh the scan
@@ -177,15 +205,17 @@ export function VectorHealthPanel({ agentId, projectId }: Props) {
         if (scan) void runScan();
       }
     } catch (err) {
-      setError(err instanceof Error ? err.message : 'Action failed');
+      if (mine === epoch.current) { if (action === 'repair-pending') setPendingPaused(true); setError(err instanceof Error ? err.message : 'Action failed'); }
     } finally {
-      setActionLoading(false);
+      if (mine === epoch.current) setActionLoading(false);
     }
-  }, [agentId, projectId, dryRun, retentionHours, fetchReport, confirmingAction, report, scan, runScan]);
+  }, [client, agentId, projectId, dryRun, retentionHours, fetchReport, confirmingAction, report, scan, runScan]);
 
   // Auto-load on mount
   useEffect(() => {
+    epoch.current++; stop.current = true; pendingCursor.current = undefined; setPendingPaused(false); setActionLoading(false); setActionResult(null); setReport(null); setScan(null); setError(null);
     void fetchReport();
+    return () => { epoch.current++; stop.current = true; };
   }, [fetchReport]);
 
   // Clean up confirm timer on unmount.
@@ -209,6 +239,8 @@ export function VectorHealthPanel({ agentId, projectId }: Props) {
 
   return (
     <div className="space-y-3 px-2 pb-2">
+      {actionLoading && lastActionKind === 'repair-pending' ? <button type="button" onClick={() => { stop.current = true; }} className="text-xs text-amber-200">Stop after this batch</button> : null}
+      {canWrite && pendingPaused && !actionLoading ? <button type="button" onClick={() => void runAction('repair-pending')} className="text-xs text-amber-200">{pendingCursor.current ? 'Continue available repair' : 'Retry repair'}</button> : null}
       {/* Description */}
       <div className="text-[10px] text-white/40 italic leading-relaxed">
         Cleanup tool for the vector index. Removes leftover records:{' '}
@@ -368,7 +400,6 @@ export function VectorHealthPanel({ agentId, projectId }: Props) {
                 size="sm"
                 skill="manage-sources"
                 packageId="@neuralis/brain-core"
-                scripts={["scripts/sync-status.sh", "scripts/reindex.sh"]}
                 label="Inspect sync status or reindex a source with the agent"
                 icon="Database"
               />
@@ -376,13 +407,13 @@ export function VectorHealthPanel({ agentId, projectId }: Props) {
             <div className="flex items-center gap-3">
               <label className="inline-flex items-center gap-1 text-[10px] text-white/60 cursor-pointer"
                 title="Preview only — nothing will be deleted.">
-                <input type="checkbox" checked={dryRun} onChange={(e) => setDryRun(e.target.checked)} className="accent-emerald-400 h-3 w-3" />
+                <input type="checkbox" disabled={actionLoading} checked={dryRun} onChange={(e) => setDryRun(e.target.checked)} className="accent-emerald-400 h-3 w-3" />
                 Dry run
               </label>
               <label className="inline-flex items-center gap-1 text-[10px] text-white/60"
                 title="Records marked as deleted within this many hours are kept (GC ignores them).">
                 Retention:
-                <input type="number" min={1} value={retentionHours}
+                <input type="number" disabled={actionLoading} min={1} value={retentionHours}
                   onChange={(e) => setRetentionHours(Math.max(1, Number(e.target.value) || 24))}
                   className="w-12 h-5 rounded px-1 text-[10px] bg-white/[0.04] border border-white/[0.08] text-white/80 outline-none" />h
               </label>