[codex] Improve workspace runtime and navigation ergonomics (#3680)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - That operator experience depends not just on issue chat, but also on
how workspaces, inbox groups, and navigation state behave over
long-running sessions
> - The current branch included a separate cluster of workspace-runtime
controls, inbox grouping, sidebar ordering, and worktree lifecycle fixes
> - Those changes cross server, shared contracts, database state, and UI
navigation, but they still form one coherent operator workflow area
> - This pull request isolates the workspace/runtime and navigation
ergonomics work into one standalone branch
> - The benefit is better workspace recovery and navigation persistence
without forcing reviewers through the unrelated issue-detail/chat work

## What Changed

- Improved execution workspace and project workspace controls, request
wiring, layout, and JSON editor ergonomics
- Hardened linked worktree reuse/startup behavior and documented the
`worktree repair` flow for recovering linked worktrees safely
- Added inbox workspace grouping, mobile collapse, archive undo,
keyboard navigation, shared group-header styling, and persisted
collapsed-group behavior
- Added persistent sidebar order preferences with the supporting DB
migration, shared/server contracts, routes, services, hooks, and UI
integration
- Scoped issue-list preferences by context and added targeted UI/server
tests for workspace controls, inbox behavior, sidebar preferences, and
worktree validation

## Verification

- `pnpm vitest run
server/src/__tests__/sidebar-preferences-routes.test.ts
ui/src/pages/Inbox.test.tsx
ui/src/components/ProjectWorkspaceSummaryCard.test.tsx
ui/src/components/WorkspaceRuntimeControls.test.tsx
ui/src/api/workspace-runtime-control.test.ts`
- `server/src/__tests__/workspace-runtime.test.ts` was attempted, but
the embedded Postgres suite self-skipped/hung on this host after
reporting an init-script issue, so it is not counted as a local pass
here

## Risks

- Medium: this branch includes migration-backed preference storage plus
worktree/runtime behavior, so merge review should pay attention to state
persistence and worktree recovery semantics
- The sidebar preference migration is standalone, but it should still be
watched for conflicts if another migration lands first

## Model Used

- OpenAI Codex coding agent (GPT-5-class runtime in Codex CLI; exact
deployed model ID is not exposed in this environment), reasoning
enabled, tool use and local code execution enabled

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [ ] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

packages/shared/src/api.ts

@@ -13,6 +13,7 @@ export const API = {
   activity: `${API_PREFIX}/activity`,
   dashboard: `${API_PREFIX}/dashboard`,
   sidebarBadges: `${API_PREFIX}/sidebar-badges`,
+  sidebarPreferences: `${API_PREFIX}/sidebar-preferences`,
   invites: `${API_PREFIX}/invites`,
   joinRequests: `${API_PREFIX}/join-requests`,
   members: `${API_PREFIX}/members`,

packages/shared/src/index.ts

@@ -232,7 +232,11 @@ export type {
   ExecutionWorkspaceCloseReadiness,
   ExecutionWorkspaceCloseReadinessState,
   ProjectWorkspaceRuntimeConfig,
+  WorkspaceCommandDefinition,
+  WorkspaceCommandKind,
+  WorkspaceRuntimeControlTarget,
   WorkspaceRuntimeService,
+  WorkspaceRuntimeServiceStateMap,
   WorkspaceOperation,
   WorkspaceOperationPhase,
   WorkspaceOperationStatus,
@@ -301,6 +305,7 @@ export type {
   DashboardSummary,
   ActivityEvent,
   SidebarBadges,
+  SidebarOrderPreference,
   InboxDismissal,
   CompanyMembership,
   PrincipalPermissionGrant,
@@ -374,6 +379,21 @@ export type {
   ProviderQuotaResult,
 } from "./types/index.js";
 
+export {
+  sidebarOrderPreferenceSchema,
+  upsertSidebarOrderPreferenceSchema,
+  type UpsertSidebarOrderPreference,
+} from "./validators/sidebar-preferences.js";
+
+export { workspaceRuntimeControlTargetSchema } from "./validators/execution-workspace.js";
+export {
+  findWorkspaceCommandDefinition,
+  listWorkspaceCommandDefinitions,
+  listWorkspaceServiceCommandDefinitions,
+  matchWorkspaceRuntimeServiceToCommand,
+  scoreWorkspaceRuntimeServiceMatch,
+} from "./workspace-commands.js";
+
 export {
   DEFAULT_FEEDBACK_DATA_SHARING_PREFERENCE,
   FEEDBACK_TARGET_TYPES,

packages/shared/src/types/index.ts

@@ -71,7 +71,11 @@ export type {
   ExecutionWorkspaceCloseReadiness,
   ExecutionWorkspaceCloseReadinessState,
   ProjectWorkspaceRuntimeConfig,
+  WorkspaceCommandDefinition,
+  WorkspaceCommandKind,
+  WorkspaceRuntimeControlTarget,
   WorkspaceRuntimeService,
+  WorkspaceRuntimeServiceStateMap,
   WorkspaceRuntimeDesiredState,
   ExecutionWorkspaceStrategyType,
   ExecutionWorkspaceMode,
@@ -165,6 +169,7 @@ export type { LiveEvent } from "./live.js";
 export type { DashboardSummary } from "./dashboard.js";
 export type { ActivityEvent } from "./activity.js";
 export type { SidebarBadges } from "./sidebar-badges.js";
+export type { SidebarOrderPreference } from "./sidebar-preferences.js";
 export type { InboxDismissal } from "./inbox-dismissal.js";
 export type {
   CompanyMembership,

packages/shared/src/types/sidebar-preferences.ts

@@ -0,0 +1,4 @@
+export interface SidebarOrderPreference {
+  orderedIds: string[];
+  updatedAt: Date | null;
+}

packages/shared/src/types/workspace-runtime.ts

@@ -46,6 +46,27 @@ export type ExecutionWorkspaceCloseActionKind =
   | "remove_local_directory";
 
 export type WorkspaceRuntimeDesiredState = "running" | "stopped";
+export type WorkspaceRuntimeServiceStateMap = Record<string, WorkspaceRuntimeDesiredState>;
+export type WorkspaceCommandKind = "service" | "job";
+
+export interface WorkspaceCommandSource {
+  type: "paperclip";
+  key: "commands" | "services" | "jobs";
+  index: number;
+}
+
+export interface WorkspaceCommandDefinition {
+  id: string;
+  name: string;
+  kind: WorkspaceCommandKind;
+  command: string | null;
+  cwd: string | null;
+  lifecycle: "shared" | "ephemeral" | null;
+  serviceIndex: number | null;
+  disabledReason: string | null;
+  rawConfig: Record<string, unknown>;
+  source: WorkspaceCommandSource;
+}
 
 export interface ExecutionWorkspaceStrategy {
   type: ExecutionWorkspaceStrategyType;
@@ -62,11 +83,19 @@ export interface ExecutionWorkspaceConfig {
   cleanupCommand: string | null;
   workspaceRuntime: Record<string, unknown> | null;
   desiredState: WorkspaceRuntimeDesiredState | null;
+  serviceStates?: WorkspaceRuntimeServiceStateMap | null;
 }
 
 export interface ProjectWorkspaceRuntimeConfig {
   workspaceRuntime: Record<string, unknown> | null;
   desiredState: WorkspaceRuntimeDesiredState | null;
+  serviceStates?: WorkspaceRuntimeServiceStateMap | null;
+}
+
+export interface WorkspaceRuntimeControlTarget {
+  workspaceCommandId?: string | null;
+  runtimeServiceId?: string | null;
+  serviceIndex?: number | null;
 }
 
 export interface ExecutionWorkspaceCloseAction {
@@ -187,6 +216,7 @@ export interface WorkspaceRuntimeService {
   stoppedAt: Date | null;
   stopPolicy: Record<string, unknown> | null;
   healthStatus: "unknown" | "healthy" | "unhealthy";
+  configIndex?: number | null;
   createdAt: Date;
   updatedAt: Date;
 }

packages/shared/src/validators/execution-workspace.ts

@@ -14,6 +14,13 @@ export const executionWorkspaceConfigSchema = z.object({
   cleanupCommand: z.string().optional().nullable(),
   workspaceRuntime: z.record(z.unknown()).optional().nullable(),
   desiredState: z.enum(["running", "stopped"]).optional().nullable(),
+  serviceStates: z.record(z.enum(["running", "stopped"])).optional().nullable(),
+}).strict();
+
+export const workspaceRuntimeControlTargetSchema = z.object({
+  workspaceCommandId: z.string().min(1).optional().nullable(),
+  runtimeServiceId: z.string().uuid().optional().nullable(),
+  serviceIndex: z.number().int().nonnegative().optional().nullable(),
 }).strict();
 
 export const executionWorkspaceCloseReadinessStateSchema = z.enum([
@@ -88,6 +95,7 @@ export const workspaceRuntimeServiceSchema = z.object({
   stoppedAt: z.coerce.date().nullable(),
   stopPolicy: z.record(z.unknown()).nullable(),
   healthStatus: z.enum(["unknown", "healthy", "unhealthy"]),
+  configIndex: z.number().int().nonnegative().nullable().optional(),
   createdAt: z.coerce.date(),
   updatedAt: z.coerce.date(),
 }).strict();

packages/shared/src/validators/index.ts

@@ -32,6 +32,11 @@ export {
   upsertIssueFeedbackVoteSchema,
   type UpsertIssueFeedbackVote,
 } from "./feedback.js";
+export {
+  sidebarOrderPreferenceSchema,
+  upsertSidebarOrderPreferenceSchema,
+  type UpsertSidebarOrderPreference,
+} from "./sidebar-preferences.js";
 export {
   companySkillSourceTypeSchema,
   companySkillTrustLevelSchema,

packages/shared/src/validators/project.ts

@@ -31,6 +31,7 @@ export const projectExecutionWorkspacePolicySchema = z
 export const projectWorkspaceRuntimeConfigSchema = z.object({
   workspaceRuntime: z.record(z.unknown()).optional().nullable(),
   desiredState: z.enum(["running", "stopped"]).optional().nullable(),
+  serviceStates: z.record(z.enum(["running", "stopped"])).optional().nullable(),
 }).strict();
 
 const projectWorkspaceSourceTypeSchema = z.enum(["local_path", "git_repo", "remote_managed", "non_git_path"]);

packages/shared/src/validators/sidebar-preferences.ts

@@ -0,0 +1,14 @@
+import { z } from "zod";
+
+const sidebarOrderedIdSchema = z.string().uuid();
+
+export const sidebarOrderPreferenceSchema = z.object({
+  orderedIds: z.array(sidebarOrderedIdSchema),
+  updatedAt: z.coerce.date().nullable(),
+});
+
+export const upsertSidebarOrderPreferenceSchema = z.object({
+  orderedIds: z.array(sidebarOrderedIdSchema),
+});
+
+export type UpsertSidebarOrderPreference = z.infer<typeof upsertSidebarOrderPreferenceSchema>;

packages/shared/src/workspace-commands.test.ts

@@ -0,0 +1,56 @@
+import { describe, expect, it } from "vitest";
+import {
+  findWorkspaceCommandDefinition,
+  listWorkspaceCommandDefinitions,
+  matchWorkspaceRuntimeServiceToCommand,
+} from "./workspace-commands.js";
+
+describe("workspace command helpers", () => {
+  it("derives service and job commands from command-first runtime config", () => {
+    const commands = listWorkspaceCommandDefinitions({
+      commands: [
+        { id: "web", name: "web", kind: "service", command: "pnpm dev" },
+        { id: "db-migrate", name: "db:migrate", kind: "job", command: "pnpm db:migrate" },
+      ],
+    });
+
+    expect(commands).toEqual([
+      expect.objectContaining({ id: "web", kind: "service", serviceIndex: 0 }),
+      expect.objectContaining({ id: "db-migrate", kind: "job", serviceIndex: null }),
+    ]);
+  });
+
+  it("falls back to legacy services and jobs arrays", () => {
+    const commands = listWorkspaceCommandDefinitions({
+      services: [{ name: "web", command: "pnpm dev" }],
+      jobs: [{ name: "lint", command: "pnpm lint" }],
+    });
+
+    expect(commands).toEqual([
+      expect.objectContaining({ id: "service:web", kind: "service", serviceIndex: 0 }),
+      expect.objectContaining({ id: "job:lint", kind: "job", serviceIndex: null }),
+    ]);
+  });
+
+  it("matches a configured service command to the current runtime service", () => {
+    const workspaceRuntime = {
+      commands: [
+        { id: "web", name: "web", kind: "service", command: "pnpm dev", cwd: "." },
+      ],
+    };
+    const command = findWorkspaceCommandDefinition(workspaceRuntime, "web");
+    expect(command).not.toBeNull();
+
+    const match = matchWorkspaceRuntimeServiceToCommand(command!, [
+      {
+        id: "runtime-web",
+        serviceName: "web",
+        command: "pnpm dev",
+        cwd: "/repo",
+        configIndex: null,
+      },
+    ]);
+
+    expect(match).toEqual(expect.objectContaining({ id: "runtime-web" }));
+  });
+});

packages/shared/src/workspace-commands.ts

@@ -0,0 +1,204 @@
+import type { WorkspaceCommandDefinition, WorkspaceRuntimeService } from "./types/workspace-runtime.js";
+
+function isRecord(value: unknown): value is Record<string, unknown> {
+  return typeof value === "object" && value !== null && !Array.isArray(value);
+}
+
+function readNonEmptyString(value: unknown): string | null {
+  if (typeof value !== "string") return null;
+  const trimmed = value.trim();
+  return trimmed.length > 0 ? trimmed : null;
+}
+
+function slugify(value: string | null | undefined) {
+  const normalized = (value ?? "")
+    .trim()
+    .toLowerCase()
+    .replace(/[^a-z0-9]+/g, "-")
+    .replace(/-+/g, "-")
+    .replace(/^-+|-+$/g, "");
+  return normalized.length > 0 ? normalized : null;
+}
+
+function deriveWorkspaceCommandId(input: {
+  kind: WorkspaceCommandDefinition["kind"];
+  explicitId: string | null;
+  name: string;
+  index: number;
+}) {
+  const explicitId = slugify(input.explicitId);
+  if (explicitId) return explicitId;
+  const nameSlug = slugify(input.name);
+  return nameSlug ? `${input.kind}:${nameSlug}` : `${input.kind}:${input.index + 1}`;
+}
+
+function buildWorkspaceCommandDefinition(input: {
+  entry: Record<string, unknown>;
+  kind: WorkspaceCommandDefinition["kind"];
+  sourceKey: WorkspaceCommandDefinition["source"]["key"];
+  sourceIndex: number;
+  serviceIndex: number | null;
+  fallbackName: string;
+}): WorkspaceCommandDefinition {
+  return {
+    id: deriveWorkspaceCommandId({
+      kind: input.kind,
+      explicitId: readNonEmptyString(input.entry.id),
+      name:
+        readNonEmptyString(input.entry.name)
+        ?? readNonEmptyString(input.entry.label)
+        ?? readNonEmptyString(input.entry.title)
+        ?? input.fallbackName,
+      index: input.sourceIndex,
+    }),
+    name:
+      readNonEmptyString(input.entry.name)
+      ?? readNonEmptyString(input.entry.label)
+      ?? readNonEmptyString(input.entry.title)
+      ?? input.fallbackName,
+    kind: input.kind,
+    command: readNonEmptyString(input.entry.command),
+    cwd: readNonEmptyString(input.entry.cwd),
+    lifecycle:
+      input.kind === "service"
+        ? input.entry.lifecycle === "ephemeral"
+          ? "ephemeral"
+          : "shared"
+        : null,
+    serviceIndex: input.serviceIndex,
+    disabledReason: readNonEmptyString(input.entry.disabledReason),
+    rawConfig: { ...input.entry },
+    source: {
+      type: "paperclip",
+      key: input.sourceKey,
+      index: input.sourceIndex,
+    },
+  };
+}
+
+function uniqueWorkspaceCommandId(
+  seen: Set<string>,
+  commandId: string,
+  sourceKey: WorkspaceCommandDefinition["source"]["key"],
+  sourceIndex: number,
+) {
+  if (!seen.has(commandId)) {
+    seen.add(commandId);
+    return commandId;
+  }
+  const fallbackId = `${commandId}-${sourceKey}-${sourceIndex + 1}`;
+  seen.add(fallbackId);
+  return fallbackId;
+}
+
+function readCommandEntries(
+  workspaceRuntime: Record<string, unknown> | null | undefined,
+  key: "commands" | "services" | "jobs",
+) {
+  const raw = workspaceRuntime?.[key];
+  return Array.isArray(raw) ? raw.filter((entry): entry is Record<string, unknown> => isRecord(entry)) : [];
+}
+
+export function listWorkspaceCommandDefinitions(
+  workspaceRuntime: Record<string, unknown> | null | undefined,
+): WorkspaceCommandDefinition[] {
+  if (!workspaceRuntime) return [];
+
+  const commandEntries = readCommandEntries(workspaceRuntime, "commands");
+  const seenIds = new Set<string>();
+  let nextServiceIndex = 0;
+
+  const finalize = (command: WorkspaceCommandDefinition) => ({
+    ...command,
+    id: uniqueWorkspaceCommandId(seenIds, command.id, command.source.key, command.source.index),
+  });
+
+  if (commandEntries.length > 0) {
+    return commandEntries.map((entry, index) =>
+      finalize(buildWorkspaceCommandDefinition({
+        entry,
+        kind: entry.kind === "job" ? "job" : "service",
+        sourceKey: "commands",
+        sourceIndex: index,
+        serviceIndex: entry.kind === "job" ? null : nextServiceIndex++,
+        fallbackName: entry.kind === "job" ? `Job ${index + 1}` : `Service ${index + 1}`,
+      })));
+  }
+
+  const serviceDefinitions = readCommandEntries(workspaceRuntime, "services").map((entry, index) =>
+    finalize(buildWorkspaceCommandDefinition({
+      entry,
+      kind: "service",
+      sourceKey: "services",
+      sourceIndex: index,
+      serviceIndex: nextServiceIndex++,
+      fallbackName: `Service ${index + 1}`,
+    })));
+  const jobDefinitions = readCommandEntries(workspaceRuntime, "jobs").map((entry, index) =>
+    finalize(buildWorkspaceCommandDefinition({
+      entry,
+      kind: "job",
+      sourceKey: "jobs",
+      sourceIndex: index,
+      serviceIndex: null,
+      fallbackName: `Job ${index + 1}`,
+    })));
+
+  return [...serviceDefinitions, ...jobDefinitions];
+}
+
+export function listWorkspaceServiceCommandDefinitions(
+  workspaceRuntime: Record<string, unknown> | null | undefined,
+) {
+  return listWorkspaceCommandDefinitions(workspaceRuntime).filter((command) => command.kind === "service");
+}
+
+export function findWorkspaceCommandDefinition(
+  workspaceRuntime: Record<string, unknown> | null | undefined,
+  workspaceCommandId: string | null | undefined,
+) {
+  const normalizedId = readNonEmptyString(workspaceCommandId);
+  if (!normalizedId) return null;
+  return listWorkspaceCommandDefinitions(workspaceRuntime).find((command) => command.id === normalizedId) ?? null;
+}
+
+export function scoreWorkspaceRuntimeServiceMatch(
+  command: Pick<WorkspaceCommandDefinition, "serviceIndex" | "name" | "command" | "cwd">,
+  runtimeService: Pick<WorkspaceRuntimeService, "configIndex" | "serviceName" | "command" | "cwd">,
+) {
+  if (command.serviceIndex !== null && runtimeService.configIndex !== null && runtimeService.configIndex !== undefined) {
+    return runtimeService.configIndex === command.serviceIndex ? 100 : -1;
+  }
+
+  let score = 0;
+  if (runtimeService.serviceName === command.name) score += 4;
+  if ((runtimeService.command ?? null) === (command.command ?? null)) score += 4;
+  if (
+    command.cwd
+    && runtimeService.cwd
+    && (runtimeService.cwd === command.cwd || runtimeService.cwd.endsWith(`/${command.cwd}`))
+  ) {
+    score += 2;
+  }
+  return score;
+}
+
+export function matchWorkspaceRuntimeServiceToCommand<
+  T extends Pick<WorkspaceRuntimeService, "configIndex" | "serviceName" | "command" | "cwd">,
+>(
+  command: Pick<WorkspaceCommandDefinition, "serviceIndex" | "name" | "command" | "cwd">,
+  runtimeServices: T[] | null | undefined,
+) {
+  let bestMatch: T | null = null;
+  let bestScore = -1;
+
+  for (const runtimeService of runtimeServices ?? []) {
+    const score = scoreWorkspaceRuntimeServiceMatch(command, runtimeService);
+    if (score > bestScore) {
+      bestMatch = runtimeService;
+      bestScore = score;
+    }
+  }
+
+  return bestScore > 0 ? bestMatch : null;
+}