Add project-first execution workspace policies

packages/db/src/migrations/0027_tranquil_tenebrous.sql

@@ -0,0 +1,2 @@
+ALTER TABLE "issues" ADD COLUMN "execution_workspace_settings" jsonb;--> statement-breakpoint
+ALTER TABLE "projects" ADD COLUMN "execution_workspace_policy" jsonb;

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

@@ -190,6 +190,13 @@
       "when": 1773089625430,
       "tag": "0026_lying_pete_wisdom",
       "breakpoints": true
+    },
+    {
+      "idx": 27,
+      "version": "7",
+      "when": 1773150731736,
+      "tag": "0027_tranquil_tenebrous",
+      "breakpoints": true
     }
   ]
 }

packages/db/src/schema/issues.ts

@@ -40,6 +40,7 @@ export const issues = pgTable(
     requestDepth: integer("request_depth").notNull().default(0),
     billingCode: text("billing_code"),
     assigneeAdapterOverrides: jsonb("assignee_adapter_overrides").$type<Record<string, unknown>>(),
+    executionWorkspaceSettings: jsonb("execution_workspace_settings").$type<Record<string, unknown>>(),
     startedAt: timestamp("started_at", { withTimezone: true }),
     completedAt: timestamp("completed_at", { withTimezone: true }),
     cancelledAt: timestamp("cancelled_at", { withTimezone: true }),

packages/db/src/schema/projects.ts

@@ -1,4 +1,4 @@
-import { pgTable, uuid, text, timestamp, date, index } from "drizzle-orm/pg-core";
+import { pgTable, uuid, text, timestamp, date, index, jsonb } from "drizzle-orm/pg-core";
 import { companies } from "./companies.js";
 import { goals } from "./goals.js";
 import { agents } from "./agents.js";
@@ -15,6 +15,7 @@ export const projects = pgTable(
     leadAgentId: uuid("lead_agent_id").references(() => agents.id),
     targetDate: date("target_date"),
     color: text("color"),
+    executionWorkspacePolicy: jsonb("execution_workspace_policy").$type<Record<string, unknown>>(),
     archivedAt: timestamp("archived_at", { withTimezone: true }),
     createdAt: timestamp("created_at", { withTimezone: true }).notNull().defaultNow(),
     updatedAt: timestamp("updated_at", { withTimezone: true }).notNull().defaultNow(),

packages/shared/src/index.ts

@@ -78,6 +78,11 @@ export type {
   ProjectGoalRef,
   ProjectWorkspace,
   WorkspaceRuntimeService,
+  ExecutionWorkspaceStrategyType,
+  ExecutionWorkspaceMode,
+  ExecutionWorkspaceStrategy,
+  ProjectExecutionWorkspacePolicy,
+  IssueExecutionWorkspaceSettings,
   Issue,
   IssueAssigneeAdapterOverrides,
   IssueComment,
@@ -157,9 +162,11 @@ export {
   type UpdateProject,
   type CreateProjectWorkspace,
   type UpdateProjectWorkspace,
+  projectExecutionWorkspacePolicySchema,
   createIssueSchema,
   createIssueLabelSchema,
   updateIssueSchema,
+  issueExecutionWorkspaceSettingsSchema,
   checkoutIssueSchema,
   addIssueCommentSchema,
   linkIssueApprovalSchema,

packages/shared/src/types/index.ts

@@ -11,7 +11,14 @@ export type {
 } from "./agent.js";
 export type { AssetImage } from "./asset.js";
 export type { Project, ProjectGoalRef, ProjectWorkspace } from "./project.js";
-export type { WorkspaceRuntimeService } from "./workspace-runtime.js";
+export type {
+  WorkspaceRuntimeService,
+  ExecutionWorkspaceStrategyType,
+  ExecutionWorkspaceMode,
+  ExecutionWorkspaceStrategy,
+  ProjectExecutionWorkspacePolicy,
+  IssueExecutionWorkspaceSettings,
+} from "./workspace-runtime.js";
 export type {
   Issue,
   IssueAssigneeAdapterOverrides,

packages/shared/src/types/issue.ts

@@ -1,6 +1,7 @@
 import type { IssuePriority, IssueStatus } from "../constants.js";
 import type { Goal } from "./goal.js";
 import type { Project, ProjectWorkspace } from "./project.js";
+import type { IssueExecutionWorkspaceSettings } from "./workspace-runtime.js";
 
 export interface IssueAncestorProject {
   id: string;
@@ -73,6 +74,7 @@ export interface Issue {
   requestDepth: number;
   billingCode: string | null;
   assigneeAdapterOverrides: IssueAssigneeAdapterOverrides | null;
+  executionWorkspaceSettings: IssueExecutionWorkspaceSettings | null;
   startedAt: Date | null;
   completedAt: Date | null;
   cancelledAt: Date | null;

packages/shared/src/types/project.ts

@@ -1,5 +1,5 @@
 import type { ProjectStatus } from "../constants.js";
-import type { WorkspaceRuntimeService } from "./workspace-runtime.js";
+import type { ProjectExecutionWorkspacePolicy, WorkspaceRuntimeService } from "./workspace-runtime.js";
 
 export interface ProjectGoalRef {
   id: string;
@@ -35,6 +35,7 @@ export interface Project {
   leadAgentId: string | null;
   targetDate: string | null;
   color: string | null;
+  executionWorkspacePolicy: ProjectExecutionWorkspacePolicy | null;
   workspaces: ProjectWorkspace[];
   primaryWorkspace: ProjectWorkspace | null;
   archivedAt: Date | null;

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

@@ -1,3 +1,31 @@
+export type ExecutionWorkspaceStrategyType = "project_primary" | "git_worktree";
+
+export type ExecutionWorkspaceMode = "inherit" | "project_primary" | "isolated" | "agent_default";
+
+export interface ExecutionWorkspaceStrategy {
+  type: ExecutionWorkspaceStrategyType;
+  baseRef?: string | null;
+  branchTemplate?: string | null;
+  worktreeParentDir?: string | null;
+}
+
+export interface ProjectExecutionWorkspacePolicy {
+  enabled: boolean;
+  defaultMode?: "project_primary" | "isolated";
+  allowIssueOverride?: boolean;
+  workspaceStrategy?: ExecutionWorkspaceStrategy | null;
+  workspaceRuntime?: Record<string, unknown> | null;
+  branchPolicy?: Record<string, unknown> | null;
+  pullRequestPolicy?: Record<string, unknown> | null;
+  cleanupPolicy?: Record<string, unknown> | null;
+}
+
+export interface IssueExecutionWorkspaceSettings {
+  mode?: ExecutionWorkspaceMode;
+  workspaceStrategy?: ExecutionWorkspaceStrategy | null;
+  workspaceRuntime?: Record<string, unknown> | null;
+}
+
 export interface WorkspaceRuntimeService {
   id: string;
   companyId: string;

packages/shared/src/validators/index.ts

@@ -49,16 +49,19 @@ export {
   updateProjectSchema,
   createProjectWorkspaceSchema,
   updateProjectWorkspaceSchema,
+  projectExecutionWorkspacePolicySchema,
   type CreateProject,
   type UpdateProject,
   type CreateProjectWorkspace,
   type UpdateProjectWorkspace,
+  type ProjectExecutionWorkspacePolicy,
 } from "./project.js";
 
 export {
   createIssueSchema,
   createIssueLabelSchema,
   updateIssueSchema,
+  issueExecutionWorkspaceSettingsSchema,
   checkoutIssueSchema,
   addIssueCommentSchema,
   linkIssueApprovalSchema,
@@ -66,6 +69,7 @@ export {
   type CreateIssue,
   type CreateIssueLabel,
   type UpdateIssue,
+  type IssueExecutionWorkspaceSettings,
   type CheckoutIssue,
   type AddIssueComment,
   type LinkIssueApproval,

packages/shared/src/validators/issue.ts

@@ -1,6 +1,23 @@
 import { z } from "zod";
 import { ISSUE_PRIORITIES, ISSUE_STATUSES } from "../constants.js";
 
+const executionWorkspaceStrategySchema = z
+  .object({
+    type: z.enum(["project_primary", "git_worktree"]).optional(),
+    baseRef: z.string().optional().nullable(),
+    branchTemplate: z.string().optional().nullable(),
+    worktreeParentDir: z.string().optional().nullable(),
+  })
+  .strict();
+
+export const issueExecutionWorkspaceSettingsSchema = z
+  .object({
+    mode: z.enum(["inherit", "project_primary", "isolated", "agent_default"]).optional(),
+    workspaceStrategy: executionWorkspaceStrategySchema.optional().nullable(),
+    workspaceRuntime: z.record(z.unknown()).optional().nullable(),
+  })
+  .strict();
+
 export const issueAssigneeAdapterOverridesSchema = z
   .object({
     adapterConfig: z.record(z.unknown()).optional(),
@@ -21,6 +38,7 @@ export const createIssueSchema = z.object({
   requestDepth: z.number().int().nonnegative().optional().default(0),
   billingCode: z.string().optional().nullable(),
   assigneeAdapterOverrides: issueAssigneeAdapterOverridesSchema.optional().nullable(),
+  executionWorkspaceSettings: issueExecutionWorkspaceSettingsSchema.optional().nullable(),
   labelIds: z.array(z.string().uuid()).optional(),
 });
 
@@ -39,6 +57,7 @@ export const updateIssueSchema = createIssueSchema.partial().extend({
 });
 
 export type UpdateIssue = z.infer<typeof updateIssueSchema>;
+export type IssueExecutionWorkspaceSettings = z.infer<typeof issueExecutionWorkspaceSettingsSchema>;
 
 export const checkoutIssueSchema = z.object({
   agentId: z.string().uuid(),

packages/shared/src/validators/project.ts

@@ -1,6 +1,28 @@
 import { z } from "zod";
 import { PROJECT_STATUSES } from "../constants.js";
 
+const executionWorkspaceStrategySchema = z
+  .object({
+    type: z.enum(["project_primary", "git_worktree"]).optional(),
+    baseRef: z.string().optional().nullable(),
+    branchTemplate: z.string().optional().nullable(),
+    worktreeParentDir: z.string().optional().nullable(),
+  })
+  .strict();
+
+export const projectExecutionWorkspacePolicySchema = z
+  .object({
+    enabled: z.boolean(),
+    defaultMode: z.enum(["project_primary", "isolated"]).optional(),
+    allowIssueOverride: z.boolean().optional(),
+    workspaceStrategy: executionWorkspaceStrategySchema.optional().nullable(),
+    workspaceRuntime: z.record(z.unknown()).optional().nullable(),
+    branchPolicy: z.record(z.unknown()).optional().nullable(),
+    pullRequestPolicy: z.record(z.unknown()).optional().nullable(),
+    cleanupPolicy: z.record(z.unknown()).optional().nullable(),
+  })
+  .strict();
+
 const projectWorkspaceFields = {
   name: z.string().min(1).optional(),
   cwd: z.string().min(1).optional().nullable(),
@@ -43,6 +65,7 @@ const projectFields = {
   leadAgentId: z.string().uuid().optional().nullable(),
   targetDate: z.string().optional().nullable(),
   color: z.string().optional().nullable(),
+  executionWorkspacePolicy: projectExecutionWorkspacePolicySchema.optional().nullable(),
   archivedAt: z.string().datetime().optional().nullable(),
 };
 
@@ -56,3 +79,5 @@ export type CreateProject = z.infer<typeof createProjectSchema>;
 export const updateProjectSchema = z.object(projectFields).partial();
 
 export type UpdateProject = z.infer<typeof updateProjectSchema>;
+
+export type ProjectExecutionWorkspacePolicy = z.infer<typeof projectExecutionWorkspacePolicySchema>;

server/src/__tests__/execution-workspace-policy.test.ts

@@ -0,0 +1,137 @@
+import { describe, expect, it } from "vitest";
+import {
+  buildExecutionWorkspaceAdapterConfig,
+  defaultIssueExecutionWorkspaceSettingsForProject,
+  parseIssueExecutionWorkspaceSettings,
+  parseProjectExecutionWorkspacePolicy,
+  resolveExecutionWorkspaceMode,
+} from "../services/execution-workspace-policy.ts";
+
+describe("execution workspace policy helpers", () => {
+  it("defaults new issue settings from enabled project policy", () => {
+    expect(
+      defaultIssueExecutionWorkspaceSettingsForProject({
+        enabled: true,
+        defaultMode: "isolated",
+      }),
+    ).toEqual({ mode: "isolated" });
+    expect(
+      defaultIssueExecutionWorkspaceSettingsForProject({
+        enabled: true,
+        defaultMode: "project_primary",
+      }),
+    ).toEqual({ mode: "project_primary" });
+    expect(defaultIssueExecutionWorkspaceSettingsForProject(null)).toBeNull();
+  });
+
+  it("prefers explicit issue mode over project policy and legacy overrides", () => {
+    expect(
+      resolveExecutionWorkspaceMode({
+        projectPolicy: { enabled: true, defaultMode: "project_primary" },
+        issueSettings: { mode: "isolated" },
+        legacyUseProjectWorkspace: false,
+      }),
+    ).toBe("isolated");
+  });
+
+  it("falls back to project policy before legacy project-workspace compatibility flag", () => {
+    expect(
+      resolveExecutionWorkspaceMode({
+        projectPolicy: { enabled: true, defaultMode: "isolated" },
+        issueSettings: null,
+        legacyUseProjectWorkspace: false,
+      }),
+    ).toBe("isolated");
+    expect(
+      resolveExecutionWorkspaceMode({
+        projectPolicy: null,
+        issueSettings: null,
+        legacyUseProjectWorkspace: false,
+      }),
+    ).toBe("agent_default");
+  });
+
+  it("applies project policy strategy and runtime defaults when isolation is enabled", () => {
+    const result = buildExecutionWorkspaceAdapterConfig({
+      agentConfig: {
+        workspaceStrategy: { type: "project_primary" },
+      },
+      projectPolicy: {
+        enabled: true,
+        defaultMode: "isolated",
+        workspaceStrategy: {
+          type: "git_worktree",
+          baseRef: "origin/main",
+        },
+        workspaceRuntime: {
+          services: [{ name: "web", command: "pnpm dev" }],
+        },
+      },
+      issueSettings: null,
+      mode: "isolated",
+      legacyUseProjectWorkspace: null,
+    });
+
+    expect(result.workspaceStrategy).toEqual({
+      type: "git_worktree",
+      baseRef: "origin/main",
+    });
+    expect(result.workspaceRuntime).toEqual({
+      services: [{ name: "web", command: "pnpm dev" }],
+    });
+  });
+
+  it("clears managed workspace strategy when issue opts out to project primary or agent default", () => {
+    const baseConfig = {
+      workspaceStrategy: { type: "git_worktree", branchTemplate: "{{issue.identifier}}" },
+      workspaceRuntime: { services: [{ name: "web" }] },
+    };
+
+    expect(
+      buildExecutionWorkspaceAdapterConfig({
+        agentConfig: baseConfig,
+        projectPolicy: { enabled: true, defaultMode: "isolated" },
+        issueSettings: { mode: "project_primary" },
+        mode: "project_primary",
+        legacyUseProjectWorkspace: null,
+      }).workspaceStrategy,
+    ).toBeUndefined();
+
+    const agentDefault = buildExecutionWorkspaceAdapterConfig({
+      agentConfig: baseConfig,
+      projectPolicy: null,
+      issueSettings: { mode: "agent_default" },
+      mode: "agent_default",
+      legacyUseProjectWorkspace: null,
+    });
+    expect(agentDefault.workspaceStrategy).toBeUndefined();
+    expect(agentDefault.workspaceRuntime).toBeUndefined();
+  });
+
+  it("parses persisted JSON payloads into typed project and issue workspace settings", () => {
+    expect(
+      parseProjectExecutionWorkspacePolicy({
+        enabled: true,
+        defaultMode: "isolated",
+        workspaceStrategy: {
+          type: "git_worktree",
+          worktreeParentDir: ".paperclip/worktrees",
+        },
+      }),
+    ).toEqual({
+      enabled: true,
+      defaultMode: "isolated",
+      workspaceStrategy: {
+        type: "git_worktree",
+        worktreeParentDir: ".paperclip/worktrees",
+      },
+    });
+    expect(
+      parseIssueExecutionWorkspaceSettings({
+        mode: "project_primary",
+      }),
+    ).toEqual({
+      mode: "project_primary",
+    });
+  });
+});

server/src/services/execution-workspace-policy.ts

@@ -0,0 +1,141 @@
+import type {
+  ExecutionWorkspaceMode,
+  ExecutionWorkspaceStrategy,
+  IssueExecutionWorkspaceSettings,
+  ProjectExecutionWorkspacePolicy,
+} from "@paperclipai/shared";
+import { asString, parseObject } from "../adapters/utils.js";
+
+type ParsedExecutionWorkspaceMode = Exclude<ExecutionWorkspaceMode, "inherit">;
+
+function cloneRecord(value: Record<string, unknown> | null | undefined): Record<string, unknown> | null {
+  if (!value) return null;
+  return { ...value };
+}
+
+function parseExecutionWorkspaceStrategy(raw: unknown): ExecutionWorkspaceStrategy | null {
+  const parsed = parseObject(raw);
+  const type = asString(parsed.type, "");
+  if (type !== "project_primary" && type !== "git_worktree") {
+    return null;
+  }
+  return {
+    type,
+    ...(typeof parsed.baseRef === "string" ? { baseRef: parsed.baseRef } : {}),
+    ...(typeof parsed.branchTemplate === "string" ? { branchTemplate: parsed.branchTemplate } : {}),
+    ...(typeof parsed.worktreeParentDir === "string" ? { worktreeParentDir: parsed.worktreeParentDir } : {}),
+  };
+}
+
+export function parseProjectExecutionWorkspacePolicy(raw: unknown): ProjectExecutionWorkspacePolicy | null {
+  const parsed = parseObject(raw);
+  if (Object.keys(parsed).length === 0) return null;
+  const enabled = typeof parsed.enabled === "boolean" ? parsed.enabled : false;
+  const defaultMode = asString(parsed.defaultMode, "");
+  const allowIssueOverride =
+    typeof parsed.allowIssueOverride === "boolean" ? parsed.allowIssueOverride : undefined;
+  return {
+    enabled,
+    ...(defaultMode === "project_primary" || defaultMode === "isolated" ? { defaultMode } : {}),
+    ...(allowIssueOverride !== undefined ? { allowIssueOverride } : {}),
+    ...(parseExecutionWorkspaceStrategy(parsed.workspaceStrategy)
+      ? { workspaceStrategy: parseExecutionWorkspaceStrategy(parsed.workspaceStrategy) }
+      : {}),
+    ...(parsed.workspaceRuntime && typeof parsed.workspaceRuntime === "object" && !Array.isArray(parsed.workspaceRuntime)
+      ? { workspaceRuntime: { ...(parsed.workspaceRuntime as Record<string, unknown>) } }
+      : {}),
+    ...(parsed.branchPolicy && typeof parsed.branchPolicy === "object" && !Array.isArray(parsed.branchPolicy)
+      ? { branchPolicy: { ...(parsed.branchPolicy as Record<string, unknown>) } }
+      : {}),
+    ...(parsed.pullRequestPolicy && typeof parsed.pullRequestPolicy === "object" && !Array.isArray(parsed.pullRequestPolicy)
+      ? { pullRequestPolicy: { ...(parsed.pullRequestPolicy as Record<string, unknown>) } }
+      : {}),
+    ...(parsed.cleanupPolicy && typeof parsed.cleanupPolicy === "object" && !Array.isArray(parsed.cleanupPolicy)
+      ? { cleanupPolicy: { ...(parsed.cleanupPolicy as Record<string, unknown>) } }
+      : {}),
+  };
+}
+
+export function parseIssueExecutionWorkspaceSettings(raw: unknown): IssueExecutionWorkspaceSettings | null {
+  const parsed = parseObject(raw);
+  if (Object.keys(parsed).length === 0) return null;
+  const mode = asString(parsed.mode, "");
+  return {
+    ...(mode === "inherit" || mode === "project_primary" || mode === "isolated" || mode === "agent_default"
+      ? { mode }
+      : {}),
+    ...(parseExecutionWorkspaceStrategy(parsed.workspaceStrategy)
+      ? { workspaceStrategy: parseExecutionWorkspaceStrategy(parsed.workspaceStrategy) }
+      : {}),
+    ...(parsed.workspaceRuntime && typeof parsed.workspaceRuntime === "object" && !Array.isArray(parsed.workspaceRuntime)
+      ? { workspaceRuntime: { ...(parsed.workspaceRuntime as Record<string, unknown>) } }
+      : {}),
+  };
+}
+
+export function defaultIssueExecutionWorkspaceSettingsForProject(
+  projectPolicy: ProjectExecutionWorkspacePolicy | null,
+): IssueExecutionWorkspaceSettings | null {
+  if (!projectPolicy?.enabled) return null;
+  return {
+    mode: projectPolicy.defaultMode === "isolated" ? "isolated" : "project_primary",
+  };
+}
+
+export function resolveExecutionWorkspaceMode(input: {
+  projectPolicy: ProjectExecutionWorkspacePolicy | null;
+  issueSettings: IssueExecutionWorkspaceSettings | null;
+  legacyUseProjectWorkspace: boolean | null;
+}): ParsedExecutionWorkspaceMode {
+  const issueMode = input.issueSettings?.mode;
+  if (issueMode && issueMode !== "inherit") {
+    return issueMode;
+  }
+  if (input.projectPolicy?.enabled) {
+    return input.projectPolicy.defaultMode === "isolated" ? "isolated" : "project_primary";
+  }
+  if (input.legacyUseProjectWorkspace === false) {
+    return "agent_default";
+  }
+  return "project_primary";
+}
+
+export function buildExecutionWorkspaceAdapterConfig(input: {
+  agentConfig: Record<string, unknown>;
+  projectPolicy: ProjectExecutionWorkspacePolicy | null;
+  issueSettings: IssueExecutionWorkspaceSettings | null;
+  mode: ParsedExecutionWorkspaceMode;
+  legacyUseProjectWorkspace: boolean | null;
+}): Record<string, unknown> {
+  const nextConfig = { ...input.agentConfig };
+  const projectHasPolicy = Boolean(input.projectPolicy?.enabled);
+  const issueHasWorkspaceOverrides = Boolean(
+    input.issueSettings?.mode ||
+    input.issueSettings?.workspaceStrategy ||
+    input.issueSettings?.workspaceRuntime,
+  );
+  const hasWorkspaceControl = projectHasPolicy || issueHasWorkspaceOverrides || input.legacyUseProjectWorkspace === false;
+
+  if (hasWorkspaceControl) {
+    if (input.mode === "isolated") {
+      const strategy =
+        input.issueSettings?.workspaceStrategy ??
+        input.projectPolicy?.workspaceStrategy ??
+        parseExecutionWorkspaceStrategy(nextConfig.workspaceStrategy) ??
+        ({ type: "git_worktree" } satisfies ExecutionWorkspaceStrategy);
+      nextConfig.workspaceStrategy = strategy as unknown as Record<string, unknown>;
+    } else {
+      delete nextConfig.workspaceStrategy;
+    }
+
+    if (input.mode === "agent_default") {
+      delete nextConfig.workspaceRuntime;
+    } else if (input.issueSettings?.workspaceRuntime) {
+      nextConfig.workspaceRuntime = cloneRecord(input.issueSettings.workspaceRuntime) ?? undefined;
+    } else if (input.projectPolicy?.workspaceRuntime) {
+      nextConfig.workspaceRuntime = cloneRecord(input.projectPolicy.workspaceRuntime) ?? undefined;
+    }
+  }
+
+  return nextConfig;
+}

server/src/services/heartbeat.ts

@@ -11,6 +11,7 @@ import {
   heartbeatRuns,
   costEvents,
   issues,
+  projects,
   projectWorkspaces,
 } from "@paperclipai/db";
 import { conflict, notFound } from "../errors.js";
@@ -31,6 +32,12 @@ import {
   releaseRuntimeServicesForRun,
 } from "./workspace-runtime.js";
 import { issueService } from "./issues.js";
+import {
+  buildExecutionWorkspaceAdapterConfig,
+  parseIssueExecutionWorkspaceSettings,
+  parseProjectExecutionWorkspacePolicy,
+  resolveExecutionWorkspaceMode,
+} from "./execution-workspace-policy.js";
 
 const MAX_LIVE_LOG_CHUNK_BYTES = 8 * 1024;
 const HEARTBEAT_MAX_CONCURRENT_RUNS_DEFAULT = 1;
@@ -1080,8 +1087,10 @@ export function heartbeatService(db: Db) {
     const issueAssigneeConfig = issueId
       ? await db
           .select({
+            projectId: issues.projectId,
             assigneeAgentId: issues.assigneeAgentId,
             assigneeAdapterOverrides: issues.assigneeAdapterOverrides,
+            executionWorkspaceSettings: issues.executionWorkspaceSettings,
           })
           .from(issues)
           .where(and(eq(issues.id, issueId), eq(issues.companyId, agent.companyId)))
@@ -1093,6 +1102,18 @@ export function heartbeatService(db: Db) {
             issueAssigneeConfig.assigneeAdapterOverrides,
           )
         : null;
+    const issueExecutionWorkspaceSettings = parseIssueExecutionWorkspaceSettings(
+      issueAssigneeConfig?.executionWorkspaceSettings,
+    );
+    const contextProjectId = readNonEmptyString(context.projectId);
+    const executionProjectId = issueAssigneeConfig?.projectId ?? contextProjectId;
+    const projectExecutionWorkspacePolicy = executionProjectId
+      ? await db
+          .select({ executionWorkspacePolicy: projects.executionWorkspacePolicy })
+          .from(projects)
+          .where(and(eq(projects.id, executionProjectId), eq(projects.companyId, agent.companyId)))
+          .then((rows) => parseProjectExecutionWorkspacePolicy(rows[0]?.executionWorkspacePolicy))
+      : null;
     const taskSession = taskKey
       ? await getTaskSession(agent.companyId, agent.id, agent.adapterType, taskKey)
       : null;
@@ -1102,16 +1123,28 @@ export function heartbeatService(db: Db) {
     const previousSessionParams = normalizeSessionParams(
       sessionCodec.deserialize(taskSessionForRun?.sessionParamsJson ?? null),
     );
+    const config = parseObject(agent.adapterConfig);
+    const executionWorkspaceMode = resolveExecutionWorkspaceMode({
+      projectPolicy: projectExecutionWorkspacePolicy,
+      issueSettings: issueExecutionWorkspaceSettings,
+      legacyUseProjectWorkspace: issueAssigneeOverrides?.useProjectWorkspace ?? null,
+    });
     const resolvedWorkspace = await resolveWorkspaceForRun(
       agent,
       context,
       previousSessionParams,
-      { useProjectWorkspace: issueAssigneeOverrides?.useProjectWorkspace ?? null },
+      { useProjectWorkspace: executionWorkspaceMode !== "agent_default" },
     );
-    const config = parseObject(agent.adapterConfig);
+    const workspaceManagedConfig = buildExecutionWorkspaceAdapterConfig({
+      agentConfig: config,
+      projectPolicy: projectExecutionWorkspacePolicy,
+      issueSettings: issueExecutionWorkspaceSettings,
+      mode: executionWorkspaceMode,
+      legacyUseProjectWorkspace: issueAssigneeOverrides?.useProjectWorkspace ?? null,
+    });
     const mergedConfig = issueAssigneeOverrides?.adapterConfig
-      ? { ...config, ...issueAssigneeOverrides.adapterConfig }
+      ? { ...workspaceManagedConfig, ...issueAssigneeOverrides.adapterConfig }
-      : config;
+      : workspaceManagedConfig;
     const { config: resolvedConfig, secretKeys } = await secretsSvc.resolveAdapterConfigForRuntime(
       agent.companyId,
       mergedConfig,
@@ -1168,6 +1201,7 @@ export function heartbeatService(db: Db) {
     context.paperclipWorkspace = {
       cwd: executionWorkspace.cwd,
       source: executionWorkspace.source,
+      mode: executionWorkspaceMode,
       strategy: executionWorkspace.strategy,
       projectId: executionWorkspace.projectId,
       workspaceId: executionWorkspace.workspaceId,

server/src/services/issues.ts

@@ -18,6 +18,10 @@ import {
 } from "@paperclipai/db";
 import { extractProjectMentionIds } from "@paperclipai/shared";
 import { conflict, notFound, unprocessable } from "../errors.js";
+import {
+  defaultIssueExecutionWorkspaceSettingsForProject,
+  parseProjectExecutionWorkspacePolicy,
+} from "./execution-workspace-policy.js";
 
 const ALL_ISSUE_STATUSES = ["backlog", "todo", "in_progress", "in_review", "blocked", "done", "cancelled"];
 
@@ -635,6 +639,19 @@ export function issueService(db: Db) {
         throw unprocessable("in_progress issues require an assignee");
       }
       return db.transaction(async (tx) => {
+        let executionWorkspaceSettings =
+          (issueData.executionWorkspaceSettings as Record<string, unknown> | null | undefined) ?? null;
+        if (executionWorkspaceSettings == null && issueData.projectId) {
+          const project = await tx
+            .select({ executionWorkspacePolicy: projects.executionWorkspacePolicy })
+            .from(projects)
+            .where(and(eq(projects.id, issueData.projectId), eq(projects.companyId, companyId)))
+            .then((rows) => rows[0] ?? null);
+          executionWorkspaceSettings =
+            defaultIssueExecutionWorkspaceSettingsForProject(
+              parseProjectExecutionWorkspacePolicy(project?.executionWorkspacePolicy),
+            ) as Record<string, unknown> | null;
+        }
         const [company] = await tx
           .update(companies)
           .set({ issueCounter: sql`${companies.issueCounter} + 1` })
@@ -644,7 +661,13 @@ export function issueService(db: Db) {
         const issueNumber = company.issueCounter;
         const identifier = `${company.issuePrefix}-${issueNumber}`;
 
-        const values = { ...issueData, companyId, issueNumber, identifier } as typeof issues.$inferInsert;
+        const values = {
+          ...issueData,
+          ...(executionWorkspaceSettings ? { executionWorkspaceSettings } : {}),
+          companyId,
+          issueNumber,
+          identifier,
+        } as typeof issues.$inferInsert;
         if (values.status === "in_progress" && !values.startedAt) {
           values.startedAt = new Date();
         }

server/src/services/projects.ts

@@ -6,11 +6,13 @@ import {
   deriveProjectUrlKey,
   isUuidLike,
   normalizeProjectUrlKey,
+  type ProjectExecutionWorkspacePolicy,
   type ProjectGoalRef,
   type ProjectWorkspace,
   type WorkspaceRuntimeService,
 } from "@paperclipai/shared";
 import { listWorkspaceRuntimeServicesForProjectWorkspaces } from "./workspace-runtime.js";
+import { parseProjectExecutionWorkspacePolicy } from "./execution-workspace-policy.js";
 
 type ProjectRow = typeof projects.$inferSelect;
 type ProjectWorkspaceRow = typeof projectWorkspaces.$inferSelect;
@@ -26,10 +28,11 @@ type CreateWorkspaceInput = {
 };
 type UpdateWorkspaceInput = Partial<CreateWorkspaceInput>;
 
-interface ProjectWithGoals extends ProjectRow {
+interface ProjectWithGoals extends Omit<ProjectRow, "executionWorkspacePolicy"> {
   urlKey: string;
   goalIds: string[];
   goals: ProjectGoalRef[];
+  executionWorkspacePolicy: ProjectExecutionWorkspacePolicy | null;
   workspaces: ProjectWorkspace[];
   primaryWorkspace: ProjectWorkspace | null;
 }
@@ -77,6 +80,7 @@ async function attachGoals(db: Db, rows: ProjectRow[]): Promise<ProjectWithGoals
       urlKey: deriveProjectUrlKey(r.name, r.id),
       goalIds: g.map((x) => x.id),
       goals: g,
+      executionWorkspacePolicy: parseProjectExecutionWorkspacePolicy(r.executionWorkspacePolicy),
     } as ProjectWithGoals;
   });
 }

ui/src/adapters/local-workspace-runtime-fields.tsx

@@ -1,5 +1,6 @@
+import { useState } from "react";
 import type { AdapterConfigFieldsProps } from "./types";
-import { DraftInput, Field, help } from "../components/agent-config-primitives";
+import { CollapsibleSection, DraftInput, Field, help } from "../components/agent-config-primitives";
 import { RuntimeServicesJsonField } from "./runtime-json-fields";
 
 const inputClass =
@@ -48,6 +49,7 @@ export function LocalWorkspaceRuntimeFields({
   config,
   mark,
 }: AdapterConfigFieldsProps) {
+  const [open, setOpen] = useState(false);
   const existing = readWorkspaceStrategy(config);
   const strategyType = isCreate ? values!.workspaceStrategyType ?? "project_primary" : existing.type;
   const updateEditWorkspaceStrategy = (patch: Partial<typeof existing>) => {
@@ -62,75 +64,81 @@ export function LocalWorkspaceRuntimeFields({
     );
   };
   return (
-    <>
+    <CollapsibleSection
-      <Field label="Workspace strategy" hint={help.workspaceStrategy}>
+      title="Advanced Workspace Overrides"
-        <select
+      open={open}
-          className={inputClass}
+      onToggle={() => setOpen((value) => !value)}
-          value={strategyType}
+    >
-          onChange={(e) => {
+      <div className="space-y-3 pt-1">
-            const nextType = e.target.value;
+        <Field label="Workspace strategy" hint={help.workspaceStrategy}>
-            if (isCreate) {
+          <select
-              set!({ workspaceStrategyType: nextType });
+            className={inputClass}
-            } else {
+            value={strategyType}
-              updateEditWorkspaceStrategy({ type: nextType });
+            onChange={(e) => {
-            }
+              const nextType = e.target.value;
-          }}
+              if (isCreate) {
-        >
+                set!({ workspaceStrategyType: nextType });
-          <option value="project_primary">Project primary workspace</option>
+              } else {
-          <option value="git_worktree">Git worktree</option>
+                updateEditWorkspaceStrategy({ type: nextType });
-        </select>
+              }
-      </Field>
+            }}
+          >
+            <option value="project_primary">Project primary workspace</option>
+            <option value="git_worktree">Git worktree</option>
+          </select>
+        </Field>
 
-      {strategyType === "git_worktree" && (
+        {strategyType === "git_worktree" && (
-        <>
+          <>
-          <Field label="Base ref" hint={help.workspaceBaseRef}>
+            <Field label="Base ref" hint={help.workspaceBaseRef}>
-            <DraftInput
+              <DraftInput
-              value={isCreate ? values!.workspaceBaseRef ?? "" : existing.baseRef}
+                value={isCreate ? values!.workspaceBaseRef ?? "" : existing.baseRef}
-              onCommit={(v) =>
+                onCommit={(v) =>
-                isCreate
+                  isCreate
-                  ? set!({ workspaceBaseRef: v })
+                    ? set!({ workspaceBaseRef: v })
-                  : updateEditWorkspaceStrategy({ baseRef: v || "" })
+                    : updateEditWorkspaceStrategy({ baseRef: v || "" })
-              }
+                }
-              immediate
+                immediate
-              className={inputClass}
+                className={inputClass}
-              placeholder="origin/main"
+                placeholder="origin/main"
-            />
+              />
-          </Field>
+            </Field>
-          <Field label="Branch template" hint={help.workspaceBranchTemplate}>
+            <Field label="Branch template" hint={help.workspaceBranchTemplate}>
-            <DraftInput
+              <DraftInput
-              value={isCreate ? values!.workspaceBranchTemplate ?? "" : existing.branchTemplate}
+                value={isCreate ? values!.workspaceBranchTemplate ?? "" : existing.branchTemplate}
-              onCommit={(v) =>
+                onCommit={(v) =>
-                isCreate
+                  isCreate
-                  ? set!({ workspaceBranchTemplate: v })
+                    ? set!({ workspaceBranchTemplate: v })
-                  : updateEditWorkspaceStrategy({ branchTemplate: v || "" })
+                    : updateEditWorkspaceStrategy({ branchTemplate: v || "" })
-              }
+                }
-              immediate
+                immediate
-              className={inputClass}
+                className={inputClass}
-              placeholder="{{issue.identifier}}-{{slug}}"
+                placeholder="{{issue.identifier}}-{{slug}}"
-            />
+              />
-          </Field>
+            </Field>
-          <Field label="Worktree parent dir" hint={help.worktreeParentDir}>
+            <Field label="Worktree parent dir" hint={help.worktreeParentDir}>
-            <DraftInput
+              <DraftInput
-              value={isCreate ? values!.worktreeParentDir ?? "" : existing.worktreeParentDir}
+                value={isCreate ? values!.worktreeParentDir ?? "" : existing.worktreeParentDir}
-              onCommit={(v) =>
+                onCommit={(v) =>
-                isCreate
+                  isCreate
-                  ? set!({ worktreeParentDir: v })
+                    ? set!({ worktreeParentDir: v })
-                  : updateEditWorkspaceStrategy({ worktreeParentDir: v || "" })
+                    : updateEditWorkspaceStrategy({ worktreeParentDir: v || "" })
-              }
+                }
-              immediate
+                immediate
-              className={inputClass}
+                className={inputClass}
-              placeholder=".paperclip/worktrees"
+                placeholder=".paperclip/worktrees"
-            />
+              />
-          </Field>
+            </Field>
-        </>
+          </>
-      )}
+        )}
-      <RuntimeServicesJsonField
+        <RuntimeServicesJsonField
-        isCreate={isCreate}
+          isCreate={isCreate}
-        values={values}
+          values={values}
-        set={set}
+          set={set}
-        config={config}
+          config={config}
-        mark={mark}
+          mark={mark}
-      />
+        />
-    </>
+      </div>
+    </CollapsibleSection>
   );
 }

ui/src/components/IssueProperties.tsx

@@ -176,6 +176,16 @@ export function IssueProperties({ issue, onUpdate, inline }: IssuePropertiesProp
     const project = orderedProjects.find((p) => p.id === id);
     return project?.name ?? id.slice(0, 8);
   };
+  const currentProject = issue.projectId
+    ? orderedProjects.find((project) => project.id === issue.projectId) ?? null
+    : null;
+  const currentProjectExecutionWorkspacePolicy = currentProject?.executionWorkspacePolicy ?? null;
+  const currentProjectSupportsExecutionWorkspace = Boolean(currentProjectExecutionWorkspacePolicy?.enabled);
+  const usesIsolatedExecutionWorkspace = issue.executionWorkspaceSettings?.mode === "isolated"
+    ? true
+    : issue.executionWorkspaceSettings?.mode === "project_primary"
+      ? false
+      : currentProjectExecutionWorkspacePolicy?.defaultMode === "isolated";
   const projectLink = (id: string | null) => {
     if (!id) return null;
     const project = projects?.find((p) => p.id === id) ?? null;
@@ -402,7 +412,10 @@ export function IssueProperties({ issue, onUpdate, inline }: IssuePropertiesProp
             "flex items-center gap-2 w-full px-2 py-1.5 text-xs rounded hover:bg-accent/50 whitespace-nowrap",
             !issue.projectId && "bg-accent"
           )}
-          onClick={() => { onUpdate({ projectId: null }); setProjectOpen(false); }}
+          onClick={() => {
+            onUpdate({ projectId: null, executionWorkspaceSettings: null });
+            setProjectOpen(false);
+          }}
         >
           No project
         </button>
@@ -419,7 +432,15 @@ export function IssueProperties({ issue, onUpdate, inline }: IssuePropertiesProp
               "flex items-center gap-2 w-full px-2 py-1.5 text-xs rounded hover:bg-accent/50 whitespace-nowrap",
               p.id === issue.projectId && "bg-accent"
             )}
-            onClick={() => { onUpdate({ projectId: p.id }); setProjectOpen(false); }}
+            onClick={() => {
+              onUpdate({
+                projectId: p.id,
+                executionWorkspaceSettings: p.executionWorkspacePolicy?.enabled
+                  ? { mode: p.executionWorkspacePolicy.defaultMode === "isolated" ? "isolated" : "project_primary" }
+                  : null,
+              });
+              setProjectOpen(false);
+            }}
           >
             <span
               className="shrink-0 h-3 w-3 rounded-sm"
@@ -504,6 +525,42 @@ export function IssueProperties({ issue, onUpdate, inline }: IssuePropertiesProp
           {projectContent}
         </PropertyPicker>
 
+        {currentProjectSupportsExecutionWorkspace && (
+          <PropertyRow label="Workspace">
+            <div className="flex items-center justify-between gap-3 rounded-md border border-border px-2 py-1.5 w-full">
+              <div className="min-w-0">
+                <div className="text-sm">
+                  {usesIsolatedExecutionWorkspace ? "Isolated issue checkout" : "Project primary checkout"}
+                </div>
+                <div className="text-[11px] text-muted-foreground">
+                  Toggle whether this issue runs in its own execution workspace.
+                </div>
+              </div>
+              <button
+                className={cn(
+                  "relative inline-flex h-5 w-9 items-center rounded-full transition-colors",
+                  usesIsolatedExecutionWorkspace ? "bg-green-600" : "bg-muted",
+                )}
+                type="button"
+                onClick={() =>
+                  onUpdate({
+                    executionWorkspaceSettings: {
+                      mode: usesIsolatedExecutionWorkspace ? "project_primary" : "isolated",
+                    },
+                  })
+                }
+              >
+                <span
+                  className={cn(
+                    "inline-block h-3.5 w-3.5 rounded-full bg-white transition-transform",
+                    usesIsolatedExecutionWorkspace ? "translate-x-4.5" : "translate-x-0.5",
+                  )}
+                />
+              </button>
+            </div>
+          </PropertyRow>
+        )}
+
         {issue.parentId && (
           <PropertyRow label="Parent">
             <Link

ui/src/components/NewIssueDialog.tsx

@@ -65,7 +65,7 @@ interface IssueDraft {
   assigneeModelOverride: string;
   assigneeThinkingEffort: string;
   assigneeChrome: boolean;
-  assigneeUseProjectWorkspace: boolean;
+  useIsolatedExecutionWorkspace: boolean;
 }
 
 const ISSUE_OVERRIDE_ADAPTER_TYPES = new Set(["claude_local", "codex_local", "opencode_local"]);
@@ -99,7 +99,6 @@ function buildAssigneeAdapterOverrides(input: {
   modelOverride: string;
   thinkingEffortOverride: string;
   chrome: boolean;
-  useProjectWorkspace: boolean;
 }): Record<string, unknown> | null {
   const adapterType = input.adapterType ?? null;
   if (!adapterType || !ISSUE_OVERRIDE_ADAPTER_TYPES.has(adapterType)) {
@@ -127,9 +126,6 @@ function buildAssigneeAdapterOverrides(input: {
   if (Object.keys(adapterConfig).length > 0) {
     overrides.adapterConfig = adapterConfig;
   }
-  if (!input.useProjectWorkspace) {
-    overrides.useProjectWorkspace = false;
-  }
   return Object.keys(overrides).length > 0 ? overrides : null;
 }
 
@@ -180,10 +176,11 @@ export function NewIssueDialog() {
   const [assigneeModelOverride, setAssigneeModelOverride] = useState("");
   const [assigneeThinkingEffort, setAssigneeThinkingEffort] = useState("");
   const [assigneeChrome, setAssigneeChrome] = useState(false);
-  const [assigneeUseProjectWorkspace, setAssigneeUseProjectWorkspace] = useState(true);
+  const [useIsolatedExecutionWorkspace, setUseIsolatedExecutionWorkspace] = useState(false);
   const [expanded, setExpanded] = useState(false);
   const [dialogCompanyId, setDialogCompanyId] = useState<string | null>(null);
   const draftTimer = useRef<ReturnType<typeof setTimeout> | null>(null);
+  const executionWorkspaceDefaultProjectId = useRef<string | null>(null);
 
   const effectiveCompanyId = dialogCompanyId ?? selectedCompanyId;
   const dialogCompany = companies.find((c) => c.id === effectiveCompanyId) ?? selectedCompany;
@@ -300,7 +297,7 @@ export function NewIssueDialog() {
       assigneeModelOverride,
       assigneeThinkingEffort,
       assigneeChrome,
-      assigneeUseProjectWorkspace,
+      useIsolatedExecutionWorkspace,
     });
   }, [
     title,
@@ -312,7 +309,7 @@ export function NewIssueDialog() {
     assigneeModelOverride,
     assigneeThinkingEffort,
     assigneeChrome,
-    assigneeUseProjectWorkspace,
+    useIsolatedExecutionWorkspace,
     newIssueOpen,
     scheduleSave,
   ]);
@@ -321,6 +318,7 @@ export function NewIssueDialog() {
   useEffect(() => {
     if (!newIssueOpen) return;
     setDialogCompanyId(selectedCompanyId);
+    executionWorkspaceDefaultProjectId.current = null;
 
     const draft = loadDraft();
     if (newIssueDefaults.title) {
@@ -333,7 +331,7 @@ export function NewIssueDialog() {
       setAssigneeModelOverride("");
       setAssigneeThinkingEffort("");
       setAssigneeChrome(false);
-      setAssigneeUseProjectWorkspace(true);
+      setUseIsolatedExecutionWorkspace(false);
     } else if (draft && draft.title.trim()) {
       setTitle(draft.title);
       setDescription(draft.description);
@@ -344,7 +342,7 @@ export function NewIssueDialog() {
       setAssigneeModelOverride(draft.assigneeModelOverride ?? "");
       setAssigneeThinkingEffort(draft.assigneeThinkingEffort ?? "");
       setAssigneeChrome(draft.assigneeChrome ?? false);
-      setAssigneeUseProjectWorkspace(draft.assigneeUseProjectWorkspace ?? true);
+      setUseIsolatedExecutionWorkspace(draft.useIsolatedExecutionWorkspace ?? false);
     } else {
       setStatus(newIssueDefaults.status ?? "todo");
       setPriority(newIssueDefaults.priority ?? "");
@@ -353,7 +351,7 @@ export function NewIssueDialog() {
       setAssigneeModelOverride("");
       setAssigneeThinkingEffort("");
       setAssigneeChrome(false);
-      setAssigneeUseProjectWorkspace(true);
+      setUseIsolatedExecutionWorkspace(false);
     }
   }, [newIssueOpen, newIssueDefaults]);
 
@@ -363,7 +361,6 @@ export function NewIssueDialog() {
       setAssigneeModelOverride("");
       setAssigneeThinkingEffort("");
       setAssigneeChrome(false);
-      setAssigneeUseProjectWorkspace(true);
       return;
     }
 
@@ -396,10 +393,11 @@ export function NewIssueDialog() {
     setAssigneeModelOverride("");
     setAssigneeThinkingEffort("");
     setAssigneeChrome(false);
-    setAssigneeUseProjectWorkspace(true);
+    setUseIsolatedExecutionWorkspace(false);
     setExpanded(false);
     setDialogCompanyId(null);
     setCompanyOpen(false);
+    executionWorkspaceDefaultProjectId.current = null;
   }
 
   function handleCompanyChange(companyId: string) {
@@ -410,7 +408,7 @@ export function NewIssueDialog() {
     setAssigneeModelOverride("");
     setAssigneeThinkingEffort("");
     setAssigneeChrome(false);
-    setAssigneeUseProjectWorkspace(true);
+    setUseIsolatedExecutionWorkspace(false);
   }
 
   function discardDraft() {
@@ -426,8 +424,14 @@ export function NewIssueDialog() {
       modelOverride: assigneeModelOverride,
       thinkingEffortOverride: assigneeThinkingEffort,
       chrome: assigneeChrome,
-      useProjectWorkspace: assigneeUseProjectWorkspace,
     });
+    const selectedProject = orderedProjects.find((project) => project.id === projectId);
+    const executionWorkspacePolicy = selectedProject?.executionWorkspacePolicy;
+    const executionWorkspaceSettings = executionWorkspacePolicy?.enabled
+      ? {
+          mode: useIsolatedExecutionWorkspace ? "isolated" : "project_primary",
+        }
+      : null;
     createIssue.mutate({
       companyId: effectiveCompanyId,
       title: title.trim(),
@@ -437,6 +441,7 @@ export function NewIssueDialog() {
       ...(assigneeId ? { assigneeAgentId: assigneeId } : {}),
       ...(projectId ? { projectId } : {}),
       ...(assigneeAdapterOverrides ? { assigneeAdapterOverrides } : {}),
+      ...(executionWorkspaceSettings ? { executionWorkspaceSettings } : {}),
     });
   }
 
@@ -467,6 +472,8 @@ export function NewIssueDialog() {
   const currentPriority = priorities.find((p) => p.value === priority);
   const currentAssignee = (agents ?? []).find((a) => a.id === assigneeId);
   const currentProject = orderedProjects.find((project) => project.id === projectId);
+  const currentProjectExecutionWorkspacePolicy = currentProject?.executionWorkspacePolicy ?? null;
+  const currentProjectSupportsExecutionWorkspace = Boolean(currentProjectExecutionWorkspacePolicy?.enabled);
   const assigneeOptionsTitle =
     assigneeAdapterType === "claude_local"
       ? "Claude options"
@@ -503,6 +510,26 @@ export function NewIssueDialog() {
       })),
     [orderedProjects],
   );
+
+  const handleProjectChange = useCallback((nextProjectId: string) => {
+    setProjectId(nextProjectId);
+    const nextProject = orderedProjects.find((project) => project.id === nextProjectId);
+    const policy = nextProject?.executionWorkspacePolicy;
+    executionWorkspaceDefaultProjectId.current = nextProjectId || null;
+    setUseIsolatedExecutionWorkspace(Boolean(policy?.enabled && policy.defaultMode === "isolated"));
+  }, [orderedProjects]);
+
+  useEffect(() => {
+    if (!newIssueOpen || !projectId || executionWorkspaceDefaultProjectId.current === projectId) {
+      return;
+    }
+    const project = orderedProjects.find((entry) => entry.id === projectId);
+    if (!project) return;
+    executionWorkspaceDefaultProjectId.current = projectId;
+    setUseIsolatedExecutionWorkspace(
+      Boolean(project.executionWorkspacePolicy?.enabled && project.executionWorkspacePolicy.defaultMode === "isolated"),
+    );
+  }, [newIssueOpen, orderedProjects, projectId]);
   const modelOverrideOptions = useMemo<InlineEntityOption[]>(
     () => {
       return [...(assigneeAdapterModels ?? [])]
@@ -705,7 +732,7 @@ export function NewIssueDialog() {
                 noneLabel="No project"
                 searchPlaceholder="Search projects..."
                 emptyMessage="No projects found."
-                onChange={setProjectId}
+                onChange={handleProjectChange}
                 onConfirm={() => {
                   descriptionEditorRef.current?.focus();
                 }}
@@ -740,6 +767,34 @@ export function NewIssueDialog() {
           </div>
         </div>
 
+        {currentProjectSupportsExecutionWorkspace && (
+          <div className="px-4 pb-2 shrink-0">
+            <div className="flex items-center justify-between rounded-md border border-border px-3 py-2">
+              <div className="space-y-0.5">
+                <div className="text-xs font-medium">Use isolated issue checkout</div>
+                <div className="text-[11px] text-muted-foreground">
+                  Create an issue-specific execution workspace instead of using the project's primary checkout.
+                </div>
+              </div>
+              <button
+                className={cn(
+                  "relative inline-flex h-5 w-9 items-center rounded-full transition-colors",
+                  useIsolatedExecutionWorkspace ? "bg-green-600" : "bg-muted",
+                )}
+                onClick={() => setUseIsolatedExecutionWorkspace((value) => !value)}
+                type="button"
+              >
+                <span
+                  className={cn(
+                    "inline-block h-3.5 w-3.5 rounded-full bg-white transition-transform",
+                    useIsolatedExecutionWorkspace ? "translate-x-4.5" : "translate-x-0.5",
+                  )}
+                />
+              </button>
+            </div>
+          </div>
+        )}
+
         {supportsAssigneeOverrides && (
           <div className="px-4 pb-2 shrink-0">
             <button
@@ -800,23 +855,6 @@ export function NewIssueDialog() {
                     </button>
                   </div>
                 )}
-                <div className="flex items-center justify-between rounded-md border border-border px-2 py-1.5">
-                  <div className="text-xs text-muted-foreground">Use project workspace</div>
-                  <button
-                    className={cn(
-                      "relative inline-flex h-5 w-9 items-center rounded-full transition-colors",
-                      assigneeUseProjectWorkspace ? "bg-green-600" : "bg-muted"
-                    )}
-                    onClick={() => setAssigneeUseProjectWorkspace((value) => !value)}
-                  >
-                    <span
-                      className={cn(
-                        "inline-block h-3.5 w-3.5 rounded-full bg-white transition-transform",
-                        assigneeUseProjectWorkspace ? "translate-x-4.5" : "translate-x-0.5"
-                      )}
-                    />
-                  </button>
-                </div>
               </div>
             )}
           </div>

ui/src/components/ProjectProperties.tsx

@@ -15,6 +15,7 @@ import { Popover, PopoverContent, PopoverTrigger } from "@/components/ui/popover
 import { Tooltip, TooltipContent, TooltipTrigger } from "@/components/ui/tooltip";
 import { ExternalLink, Github, Plus, Trash2, X } from "lucide-react";
 import { ChoosePathButton } from "./PathInstructionsModal";
+import { CollapsibleSection, DraftInput } from "./agent-config-primitives";
 
 const PROJECT_STATUSES = [
   { value: "backlog", label: "Backlog" },
@@ -80,6 +81,7 @@ export function ProjectProperties({ project, onUpdate }: ProjectPropertiesProps)
   const { selectedCompanyId } = useCompany();
   const queryClient = useQueryClient();
   const [goalOpen, setGoalOpen] = useState(false);
+  const [executionWorkspaceAdvancedOpen, setExecutionWorkspaceAdvancedOpen] = useState(false);
   const [workspaceMode, setWorkspaceMode] = useState<"local" | "repo" | null>(null);
   const [workspaceCwd, setWorkspaceCwd] = useState("");
   const [workspaceRepoUrl, setWorkspaceRepoUrl] = useState("");
@@ -106,6 +108,16 @@ export function ProjectProperties({ project, onUpdate }: ProjectPropertiesProps)
 
   const availableGoals = (allGoals ?? []).filter((g) => !linkedGoalIds.includes(g.id));
   const workspaces = project.workspaces ?? [];
+  const executionWorkspacePolicy = project.executionWorkspacePolicy ?? null;
+  const executionWorkspacesEnabled = executionWorkspacePolicy?.enabled === true;
+  const executionWorkspaceDefaultMode =
+    executionWorkspacePolicy?.defaultMode === "isolated" ? "isolated" : "project_primary";
+  const executionWorkspaceStrategy = executionWorkspacePolicy?.workspaceStrategy ?? {
+    type: "git_worktree",
+    baseRef: "",
+    branchTemplate: "",
+    worktreeParentDir: "",
+  };
 
   const invalidateProject = () => {
     queryClient.invalidateQueries({ queryKey: queryKeys.projects.detail(project.id) });
@@ -146,6 +158,19 @@ export function ProjectProperties({ project, onUpdate }: ProjectPropertiesProps)
     setGoalOpen(false);
   };
 
+  const updateExecutionWorkspacePolicy = (patch: Record<string, unknown>) => {
+    if (!onUpdate) return;
+    onUpdate({
+      executionWorkspacePolicy: {
+        enabled: executionWorkspacesEnabled,
+        defaultMode: executionWorkspaceDefaultMode,
+        allowIssueOverride: executionWorkspacePolicy?.allowIssueOverride ?? true,
+        ...executionWorkspacePolicy,
+        ...patch,
+      },
+    });
+  };
+
   const isAbsolutePath = (value: string) => value.startsWith("/") || /^[A-Za-z]:[\\/]/.test(value);
 
   const isGitHubRepoUrl = (value: string) => {
@@ -346,6 +371,162 @@ export function ProjectProperties({ project, onUpdate }: ProjectPropertiesProps)
       <Separator />
 
       <div className="space-y-1">
+        <div className="py-1.5 space-y-2">
+          <div className="flex items-center gap-1.5 text-xs text-muted-foreground">
+            <span>Execution Workspaces</span>
+            <Tooltip>
+              <TooltipTrigger asChild>
+                <button
+                  type="button"
+                  className="inline-flex h-4 w-4 items-center justify-center rounded-full border border-border text-[10px] text-muted-foreground hover:text-foreground"
+                  aria-label="Execution workspaces help"
+                >
+                  ?
+                </button>
+              </TooltipTrigger>
+              <TooltipContent side="top">
+                Project-owned defaults for isolated issue checkouts and execution workspace behavior.
+              </TooltipContent>
+            </Tooltip>
+          </div>
+          <div className="rounded-md border border-border p-3 space-y-3">
+            <div className="flex items-center justify-between gap-3">
+              <div className="space-y-0.5">
+                <div className="text-sm font-medium">Enable isolated issue checkouts</div>
+                <div className="text-xs text-muted-foreground">
+                  Let issues choose between the project’s primary checkout and an isolated execution workspace.
+                </div>
+              </div>
+              {onUpdate ? (
+                <button
+                  className={cn(
+                    "relative inline-flex h-5 w-9 items-center rounded-full transition-colors",
+                    executionWorkspacesEnabled ? "bg-green-600" : "bg-muted",
+                  )}
+                  type="button"
+                  onClick={() => updateExecutionWorkspacePolicy({ enabled: !executionWorkspacesEnabled })}
+                >
+                  <span
+                    className={cn(
+                      "inline-block h-3.5 w-3.5 rounded-full bg-white transition-transform",
+                      executionWorkspacesEnabled ? "translate-x-4.5" : "translate-x-0.5",
+                    )}
+                  />
+                </button>
+              ) : (
+                <span className="text-xs text-muted-foreground">
+                  {executionWorkspacesEnabled ? "Enabled" : "Disabled"}
+                </span>
+              )}
+            </div>
+
+            {executionWorkspacesEnabled && (
+              <>
+                <div className="flex items-center justify-between gap-3 rounded-md border border-border/70 px-3 py-2">
+                  <div className="space-y-0.5">
+                    <div className="text-sm">New issues default to isolated checkout</div>
+                    <div className="text-[11px] text-muted-foreground">
+                      If disabled, new issues stay on the project’s primary checkout unless someone opts in.
+                    </div>
+                  </div>
+                  <button
+                    className={cn(
+                      "relative inline-flex h-5 w-9 items-center rounded-full transition-colors",
+                      executionWorkspaceDefaultMode === "isolated" ? "bg-green-600" : "bg-muted",
+                    )}
+                    type="button"
+                    onClick={() =>
+                      updateExecutionWorkspacePolicy({
+                        defaultMode: executionWorkspaceDefaultMode === "isolated" ? "project_primary" : "isolated",
+                      })}
+                  >
+                    <span
+                      className={cn(
+                        "inline-block h-3.5 w-3.5 rounded-full bg-white transition-transform",
+                        executionWorkspaceDefaultMode === "isolated" ? "translate-x-4.5" : "translate-x-0.5",
+                      )}
+                    />
+                  </button>
+                </div>
+
+                <CollapsibleSection
+                  title="Advanced Checkout Settings"
+                  open={executionWorkspaceAdvancedOpen}
+                  onToggle={() => setExecutionWorkspaceAdvancedOpen((open) => !open)}
+                >
+                  <div className="space-y-3 pt-1">
+                    <div className="rounded-md border border-border/70 px-3 py-2 text-xs text-muted-foreground">
+                      Host-managed implementation: <span className="text-foreground">Git worktree</span>
+                    </div>
+                    <div>
+                      <div className="mb-1 flex items-center gap-1.5">
+                        <label className="text-xs text-muted-foreground">Base ref</label>
+                      </div>
+                      <DraftInput
+                        value={executionWorkspaceStrategy.baseRef ?? ""}
+                        onCommit={(value) =>
+                          updateExecutionWorkspacePolicy({
+                            workspaceStrategy: {
+                              ...executionWorkspaceStrategy,
+                              type: "git_worktree",
+                              baseRef: value || null,
+                            },
+                          })}
+                        immediate
+                        className="w-full rounded border border-border bg-transparent px-2 py-1 text-xs font-mono outline-none"
+                        placeholder="origin/main"
+                      />
+                    </div>
+                    <div>
+                      <div className="mb-1 flex items-center gap-1.5">
+                        <label className="text-xs text-muted-foreground">Branch template</label>
+                      </div>
+                      <DraftInput
+                        value={executionWorkspaceStrategy.branchTemplate ?? ""}
+                        onCommit={(value) =>
+                          updateExecutionWorkspacePolicy({
+                            workspaceStrategy: {
+                              ...executionWorkspaceStrategy,
+                              type: "git_worktree",
+                              branchTemplate: value || null,
+                            },
+                          })}
+                        immediate
+                        className="w-full rounded border border-border bg-transparent px-2 py-1 text-xs font-mono outline-none"
+                        placeholder="{{issue.identifier}}-{{slug}}"
+                      />
+                    </div>
+                    <div>
+                      <div className="mb-1 flex items-center gap-1.5">
+                        <label className="text-xs text-muted-foreground">Worktree parent dir</label>
+                      </div>
+                      <DraftInput
+                        value={executionWorkspaceStrategy.worktreeParentDir ?? ""}
+                        onCommit={(value) =>
+                          updateExecutionWorkspacePolicy({
+                            workspaceStrategy: {
+                              ...executionWorkspaceStrategy,
+                              type: "git_worktree",
+                              worktreeParentDir: value || null,
+                            },
+                          })}
+                        immediate
+                        className="w-full rounded border border-border bg-transparent px-2 py-1 text-xs font-mono outline-none"
+                        placeholder=".paperclip/worktrees"
+                      />
+                    </div>
+                    <p className="text-[11px] text-muted-foreground">
+                      Runtime services stay under Paperclip control and are not configured here yet.
+                    </p>
+                  </div>
+                </CollapsibleSection>
+              </>
+            )}
+          </div>
+        </div>
+
+        <Separator />
+
         <div className="py-1.5 space-y-2">
           <div className="flex items-center gap-1.5 text-xs text-muted-foreground">
             <span>Workspaces</span>