[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/db/src/migrations/0056_spooky_ultragirl.sql

@@ -0,0 +1,22 @@
+CREATE TABLE "company_user_sidebar_preferences" (
+	"id" uuid PRIMARY KEY DEFAULT gen_random_uuid() NOT NULL,
+	"company_id" uuid NOT NULL,
+	"user_id" text NOT NULL,
+	"project_order" jsonb DEFAULT '[]'::jsonb NOT NULL,
+	"created_at" timestamp with time zone DEFAULT now() NOT NULL,
+	"updated_at" timestamp with time zone DEFAULT now() NOT NULL
+);
+--> statement-breakpoint
+CREATE TABLE "user_sidebar_preferences" (
+	"id" uuid PRIMARY KEY DEFAULT gen_random_uuid() NOT NULL,
+	"user_id" text NOT NULL,
+	"company_order" jsonb DEFAULT '[]'::jsonb NOT NULL,
+	"created_at" timestamp with time zone DEFAULT now() NOT NULL,
+	"updated_at" timestamp with time zone DEFAULT now() NOT NULL
+);
+--> statement-breakpoint
+ALTER TABLE "company_user_sidebar_preferences" ADD CONSTRAINT "company_user_sidebar_preferences_company_id_companies_id_fk" FOREIGN KEY ("company_id") REFERENCES "public"."companies"("id") ON DELETE cascade ON UPDATE no action;--> statement-breakpoint
+CREATE INDEX "company_user_sidebar_preferences_company_idx" ON "company_user_sidebar_preferences" USING btree ("company_id");--> statement-breakpoint
+CREATE INDEX "company_user_sidebar_preferences_user_idx" ON "company_user_sidebar_preferences" USING btree ("user_id");--> statement-breakpoint
+CREATE UNIQUE INDEX "company_user_sidebar_preferences_company_user_uq" ON "company_user_sidebar_preferences" USING btree ("company_id","user_id");--> statement-breakpoint
+CREATE UNIQUE INDEX "user_sidebar_preferences_user_uq" ON "user_sidebar_preferences" USING btree ("user_id");

packages/db/src/migrations/meta/_journal.json

@@ -393,6 +393,13 @@
       "when": 1775825256196,
       "tag": "0055_kind_weapon_omega",
       "breakpoints": true
+    },
+    {
+      "idx": 56,
+      "version": "7",
+      "when": 1776084034244,
+      "tag": "0056_spooky_ultragirl",
+      "breakpoints": true
     }
   ]
 }

packages/db/src/schema/company_user_sidebar_preferences.ts

@@ -0,0 +1,22 @@
+import { pgTable, uuid, text, timestamp, jsonb, uniqueIndex, index } from "drizzle-orm/pg-core";
+import { companies } from "./companies.js";
+
+export const companyUserSidebarPreferences = pgTable(
+  "company_user_sidebar_preferences",
+  {
+    id: uuid("id").primaryKey().defaultRandom(),
+    companyId: uuid("company_id").notNull().references(() => companies.id, { onDelete: "cascade" }),
+    userId: text("user_id").notNull(),
+    projectOrder: jsonb("project_order").$type<string[]>().notNull().default([]),
+    createdAt: timestamp("created_at", { withTimezone: true }).notNull().defaultNow(),
+    updatedAt: timestamp("updated_at", { withTimezone: true }).notNull().defaultNow(),
+  },
+  (table) => ({
+    companyIdx: index("company_user_sidebar_preferences_company_idx").on(table.companyId),
+    userIdx: index("company_user_sidebar_preferences_user_idx").on(table.userId),
+    companyUserUq: uniqueIndex("company_user_sidebar_preferences_company_user_uq").on(
+      table.companyId,
+      table.userId,
+    ),
+  }),
+);

packages/db/src/schema/index.ts

@@ -3,10 +3,12 @@ export { companyLogos } from "./company_logos.js";
 export { authUsers, authSessions, authAccounts, authVerifications } from "./auth.js";
 export { instanceSettings } from "./instance_settings.js";
 export { instanceUserRoles } from "./instance_user_roles.js";
+export { userSidebarPreferences } from "./user_sidebar_preferences.js";
 export { agents } from "./agents.js";
 export { boardApiKeys } from "./board_api_keys.js";
 export { cliAuthChallenges } from "./cli_auth_challenges.js";
 export { companyMemberships } from "./company_memberships.js";
+export { companyUserSidebarPreferences } from "./company_user_sidebar_preferences.js";
 export { principalPermissionGrants } from "./principal_permission_grants.js";
 export { invites } from "./invites.js";
 export { joinRequests } from "./join_requests.js";

packages/db/src/schema/user_sidebar_preferences.ts

@@ -0,0 +1,15 @@
+import { pgTable, uuid, text, timestamp, jsonb, uniqueIndex } from "drizzle-orm/pg-core";
+
+export const userSidebarPreferences = pgTable(
+  "user_sidebar_preferences",
+  {
+    id: uuid("id").primaryKey().defaultRandom(),
+    userId: text("user_id").notNull(),
+    companyOrder: jsonb("company_order").$type<string[]>().notNull().default([]),
+    createdAt: timestamp("created_at", { withTimezone: true }).notNull().defaultNow(),
+    updatedAt: timestamp("updated_at", { withTimezone: true }).notNull().defaultNow(),
+  },
+  (table) => ({
+    userUq: uniqueIndex("user_sidebar_preferences_user_uq").on(table.userId),
+  }),
+);