@markjaquith/agency 2.53.0 → 2.54.1

package/README.md

@@ -489,9 +489,10 @@ materializations, then compares every execution declaration with local branch
 and worktree registration, checkout dirtiness, resolved reference commits, claim
 expiry, and pull request state, merge state, and mergeability. It reports
 structured `changes`, `warnings`, `unresolved`, and per-execution evidence. The
-default and `--dry-run` modes are observational.
+default mode applies safe reconciliation transitions; `--dry-run` is explicitly
+observational.
 
-`agency sync --apply` performs only these safe transitions:
+`agency sync` performs only these safe transitions:
 
 - materialize declared but missing repositories from their canonical remotes;
 - adopt legacy materializations only when they have an unambiguous portable origin;
@@ -722,7 +723,7 @@ Single-phase tasks and phases store status in YAML. New execution units start
 `open`, and `agency work` marks the selected execution unit `working` immediately
 before launch. Running `agency work` again can relaunch unclaimed `working` work.
 By default, `done` requires an authoritative merged pull request and is applied
-by `agency sync --apply`. Work whose intended outcome genuinely requires no pull
+by `agency sync`. Work whose intended outcome genuinely requires no pull
 request may instead use an explicit `--no-pull-request --summary <text>` status
 transition. Agency records the summary, completion time, and optional evidence
 URL durably; reopening removes that evidence. This exceptional path refuses work
@@ -804,6 +805,7 @@ for restoration. Archived IDs are reserved until restored.
 agency work [<directory> | --epic <epic-id>] [--runner <name>] [--auto] [--print-command]
 agency work prepare [target] [--dry-run] [--json]
 agency worktree <list|inspect|prepare|remove|rebuild|repair>
+agency pr create <task-id> [phase-id] [--draft] [--force] [--json]
 agency pr [args...]
 ```
 
@@ -850,9 +852,12 @@ Agency resolves the ref to a commit and creates a detached worktree. Existing
 reference worktrees are reused only while their commit still matches the declared
 ref; use a commit SHA as `ref` when reproducibility matters.
 
-`agency pr` forwards every argument to `gh pr`. From an execution task or phase
-directory, including descendants, it runs in that execution unit's authoritative
-writable checkout. Otherwise it runs in the caller's current directory.
+Task-aware `agency pr create <task-id> [phase-id]` uses Agency's delivery flow,
+including readiness checks and durable PR recording. Other `agency pr`
+invocations forward every argument to `gh pr`. From an execution task or phase
+directory, including descendants, passthrough runs in that execution unit's
+authoritative writable checkout. Otherwise it runs in the caller's current
+directory.
 
 ### Status and Validation
 

package/cli-main.ts

@@ -5,7 +5,7 @@ import { join, resolve } from "node:path"
 import { parseCli } from "./src/cli-parser"
 import { init, help as initHelp } from "./src/commands/init"
 import { task, help as taskHelp } from "./src/commands/task"
-import { pr, help as prHelp } from "./src/commands/pr"
+import { pr, prCreate, help as prHelp } from "./src/commands/pr"
 import { work, workPrepare, help as workHelp } from "./src/commands/work"
 import { worktree, help as worktreeHelp } from "./src/commands/worktree"
 import { status, help as statusHelp } from "./src/commands/status"
@@ -134,7 +134,7 @@ const resolveInvocationCwd = (
 ) =>
 	runEffect(
 		Effect.gen(function* () {
-			if (commandName === "pr") {
+			if (commandName === "pr" && options.passthrough) {
 				return resolve(options.cwd ?? process.cwd())
 			}
 			if (
@@ -287,7 +287,22 @@ const commands: Record<string, Command> = {
 				console.log(prHelp)
 				return
 			}
-			process.exitCode = await runEffect(pr(args, options.cwd))
+			if (options.passthrough) {
+				process.exitCode = await runEffect(pr(args, options.cwd))
+				return
+			}
+			await runCommand(
+				prCreate({
+					taskId: args[1]!,
+					phaseId: args[2],
+					draft: options.draft,
+					force: options.force,
+					json: options.json,
+					silent: options.silent,
+					verbose: options.verbose,
+					cwd: options.cwd,
+				}),
+			)
 		},
 	},
 	phase: {
@@ -694,7 +709,6 @@ const commands: Record<string, Command> = {
 			}
 			await runCommand(
 				sync({
-					apply: options.apply,
 					dryRun: options["dry-run"],
 					json: options.json,
 					silent: options.silent,
@@ -727,7 +741,7 @@ Commands:
   worktree <subcommand>  Inspect and maintain managed workspaces
   vcs <subcommand>       Inspect or migrate the version-control backend
   next                   List or select ready execution units
-  pr [args...]           Run gh pr with Agency repository focus
+  pr create / pr [...]  Create an Agency PR or run gh pr with repository focus
   review refresh         Explicitly refresh a pinned review task
   repo <subcommand>      Manage workbase repositories
   status                 Show status for the current workbase
@@ -762,7 +776,7 @@ const machineMode = process.argv
 
 try {
 	const args = process.argv.slice(2)
-	const { commandName, args: commandArgs, values } = parseCli(args)
+	const { commandName, args: commandArgs, passthrough, values } = parseCli(args)
 
 	// Handle global flags
 	if (values.version) {
@@ -786,16 +800,29 @@ try {
 		!values.json &&
 		!values["no-input"] &&
 		Boolean(process.stdin.isTTY && process.stdout.isTTY)
-	const cwd = await resolveInvocationCwd(commandName, values)
+	const cwd = await resolveInvocationCwd(commandName, {
+		...values,
+		passthrough,
+	})
 	if (values.json || (values.jsonl && values.help)) {
 		const result = await collectCommandResult(() =>
-			command.run(commandArgs, { ...values, cwd, inputAllowed }),
+			command.run(commandArgs, { ...values, cwd, inputAllowed, passthrough }),
 		)
 		writeEnvelope(successEnvelope(result))
 	} else if (values.jsonl) {
-		await command.run(commandArgs, { ...values, cwd, inputAllowed: false })
+		await command.run(commandArgs, {
+			...values,
+			cwd,
+			inputAllowed: false,
+			passthrough,
+		})
 	} else {
-		await command.run(commandArgs, { ...values, cwd, inputAllowed })
+		await command.run(commandArgs, {
+			...values,
+			cwd,
+			inputAllowed,
+			passthrough,
+		})
 	}
 } catch (error) {
 	if (machineMode) {

package/fixtures/protocol/orchestration-recipes.json

@@ -30,7 +30,7 @@
   ["work", "prepare", "--task", "checkout", "--phase", "ui", "--json"],
   ["work", "tasks/checkout/phases/ui", "--runner", "opencode"],
   ["sync", "--dry-run", "--json"],
-  ["sync", "--apply", "--json"],
+  ["sync", "--json"],
   ["pr", "create", "checkout", "ui", "--json"],
   [
     "finish",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@markjaquith/agency",
-  "version": "2.53.0",
+  "version": "2.54.1",
   "description": "Manage agentic work across repositories with durable workbases",
   "keywords": [
     "agents",

package/src/cli-parser.test.ts

@@ -367,22 +367,44 @@ describe("strict CLI parsing", () => {
 		expect(parseCli(["--cwd", "/workbase", "pr", ...args])).toEqual({
 			commandName: "pr",
 			args,
+			passthrough: true,
 			values: { cwd: "/workbase" },
 		})
 	})
 
-	test("parses reconciliation modes and rejects conflicting modes", () => {
-		expect(parseCli(["sync", "--dry-run", "--json"])).toMatchObject({
+	test("parses task-aware pr create without routing it to passthrough", () => {
+		expect(
+			parseCli([
+				"pr",
+				"create",
+				"ship",
+				"release",
+				"--draft",
+				"--force",
+				"--json",
+			]),
+		).toEqual({
+			commandName: "pr",
+			args: ["create", "ship", "release"],
+			values: { draft: true, force: true, json: true },
+		})
+		const selected = parseCli(["pr", "create", "--task", "ship"])
+		expect(selected).toMatchObject({
+			args: ["create", "ship"],
+		})
+		expect(selected.passthrough).toBeUndefined()
+	})
+
+	test("parses explicit dry-run reconciliation", () => {
+		expect(parseCli(["sync"])).toMatchObject({
 			commandName: "sync",
-			values: { "dry-run": true, json: true },
+			values: {},
 		})
-		expect(parseCli(["sync", "--apply"])).toMatchObject({
+		expect(parseCli(["sync", "--dry-run", "--json"])).toMatchObject({
 			commandName: "sync",
-			values: { apply: true },
+			values: { "dry-run": true, json: true },
 		})
-		expect(() => parseCli(["sync", "--dry-run", "--apply"])).toThrow(
-			"cannot be combined",
-		)
+		expect(() => parseCli(["sync", "--apply"])).toThrow("Unknown option")
 	})
 
 	test("accepts archive dry-run", () => {

package/src/cli-parser.ts

@@ -678,18 +678,16 @@ const commands = {
 		},
 	},
 	sync: {
-		usage: "agency sync [--dry-run | --apply] [--json]",
+		usage: "agency sync [--dry-run] [--json]",
 		options: {
 			...outputOptions,
 			"dry-run": { type: "boolean" },
-			apply: { type: "boolean" },
 		},
 		command: {
-			usage: "agency sync [--dry-run | --apply] [--json]",
+			usage: "agency sync [--dry-run] [--json]",
 			minArgs: 0,
 			maxArgs: 0,
-			options: ["dry-run", "apply", "json"],
-			conflicts: [["dry-run", "apply"]],
+			options: ["dry-run", "json"],
 		},
 	},
 	archive: {
@@ -897,12 +895,22 @@ const commands = {
 		},
 	},
 	pr: {
-		usage: "agency pr [args...]",
-		options: commonOptions,
-		command: {
-			usage: "agency pr [args...]",
-			minArgs: 0,
-			maxArgs: Number.POSITIVE_INFINITY,
+		usage: "agency pr create <task-id> [phase-id] | agency pr [args...]",
+		options: {
+			...outputOptions,
+			draft: { type: "boolean" },
+			force: { type: "boolean" },
+			task: { type: "string" },
+			phase: { type: "string" },
+		},
+		subcommands: {
+			create: {
+				usage:
+					"agency pr create <task-id> [phase-id] [--draft] [--force] [--json]",
+				minArgs: 1,
+				maxArgs: 2,
+				options: ["draft", "force", "json", "task", "phase"],
+			},
 		},
 	},
 	next: {
@@ -1021,6 +1029,7 @@ const preCommandValueOptions = new Set(["--workbase", "--cwd"])
 export interface ParsedCli {
 	readonly commandName?: keyof typeof commands
 	readonly args: string[]
+	readonly passthrough?: boolean
 	readonly values: Record<
 		string,
 		boolean | string | (boolean | string)[] | undefined
@@ -1093,6 +1102,7 @@ const targetSlots = (
 	if (commandName === "worktree" && subcommand !== "list") {
 		return ["task", "phase"]
 	}
+	if (commandName === "pr" && subcommand === "create") return ["task", "phase"]
 	return []
 }
 
@@ -1313,7 +1323,15 @@ export function parseCli(args: readonly string[]): ParsedCli {
 			"agency <command> [options]",
 		)
 	}
-	if (commandName === "pr") {
+	const prArgs = args.slice(commandIndex + 1)
+	const taskAwarePrCreate =
+		commandName === "pr" &&
+		prArgs[0] === "create" &&
+		((prArgs[1] !== undefined && !prArgs[1].startsWith("-")) ||
+			prArgs.some(
+				(argument) => argument === "--task" || argument.startsWith("--task="),
+			))
+	if (commandName === "pr" && !taskAwarePrCreate) {
 		const parsed = parse(
 			args.slice(0, commandIndex),
 			rootOptions,
@@ -1338,7 +1356,8 @@ export function parseCli(args: readonly string[]): ParsedCli {
 		}
 		return {
 			commandName,
-			args: [...args.slice(commandIndex + 1)],
+			args: prArgs,
+			passthrough: true,
 			values: parsed.values,
 		}
 	}

package/src/cli.test.ts

@@ -598,6 +598,20 @@ exit 23
 				blockers: [{ kind: "status", reason: "Task status is dropped" }],
 			},
 		])
+
+		const blockedPr = await runCli(["pr", "create", "finished", "--json"], root)
+		expect(blockedPr.exitCode).toBe(1)
+		expect(blockedPr.stderr).toBe("")
+		expect(JSON.parse(blockedPr.stdout)).toMatchObject({
+			ok: false,
+			error: {
+				code: "EXECUTION_BLOCKED",
+				fields: {
+					status: "dropped",
+					blockers: [{ kind: "status", reason: "Task status is dropped" }],
+				},
+			},
+		})
 	})
 
 	test("reports and synchronizes managed integration files", async () => {

package/src/commands/claim.ts

@@ -117,6 +117,6 @@ export const finishHelp = `
 Usage: agency finish <task-id> [phase-id] --session-id <id> --revision <sha256> --outcome <done|dropped> [--no-pull-request --summary <text> [--evidence-url <url>]]
 
 Finish a claim owned by the session. A done claim outcome leaves unmerged work
-working; agency sync --apply marks the execution unit done after merge. Use
+working; agency sync marks the execution unit done after merge. Use
 --no-pull-request with a summary for an explicit non-PR completion.
 `

package/src/commands/pr.test.ts

@@ -1,8 +1,15 @@
 import { afterEach, beforeEach, describe, expect, test } from "bun:test"
+import { Effect } from "effect"
 import { chmod, mkdir, realpath } from "node:fs/promises"
 import { dirname, join } from "node:path"
-import { cleanupTempDir, createTempDir, runTestEffect } from "../test-utils"
-import { pr } from "./pr"
+import { PullRequestService } from "../services/PullRequestService"
+import {
+	captureLogs,
+	cleanupTempDir,
+	createTempDir,
+	runTestEffect,
+} from "../test-utils"
+import { pr, prCreate } from "./pr"
 
 const write = async (root: string, path: string, content: string) => {
 	const fullPath = join(root, path)
@@ -95,6 +102,39 @@ status: open
 		return root
 	}
 
+	test("creates and records an Agency pull request", async () => {
+		const url = "https://github.com/markjaquith/agency/pull/123"
+		let received: unknown[] = []
+		const logs = await captureLogs(() =>
+			Effect.runPromise(
+				prCreate({
+					taskId: "example",
+					phaseId: "implementation",
+					draft: true,
+					force: true,
+					cwd: "/workbase",
+					json: true,
+				}).pipe(
+					Effect.provideService(PullRequestService, {
+						create: (...args: unknown[]) => {
+							received = args
+							return Effect.succeed(url)
+						},
+					} as never),
+				) as Effect.Effect<void, unknown, never>,
+			),
+		)
+
+		expect(JSON.parse(logs[0]!)).toEqual({ url })
+		expect(received).toEqual([
+			"example",
+			"implementation",
+			true,
+			"/workbase",
+			expect.objectContaining({ force: true, draft: true, json: true }),
+		])
+	})
+
 	test("focuses task and descendant invocations on the writable checkout", async () => {
 		const root = await createExecutionWorkbase()
 		const task = join(root, "tasks/single")

package/src/commands/pr.ts

@@ -2,6 +2,30 @@ import { Effect } from "effect"
 import { resolve } from "node:path"
 import { ContextService } from "../services/ContextService"
 import { FileSystemService } from "../services/FileSystemService"
+import { PullRequestService } from "../services/PullRequestService"
+import type { BaseCommandOptions } from "../utils/command"
+import { createLoggers } from "../utils/effect"
+
+interface PrCreateOptions extends BaseCommandOptions {
+	readonly taskId: string
+	readonly phaseId?: string
+	readonly draft?: boolean
+	readonly force?: boolean
+}
+
+export const prCreate = (options: PrCreateOptions) =>
+	Effect.gen(function* () {
+		const pullRequests = yield* PullRequestService
+		const { log } = createLoggers(options)
+		const url = yield* pullRequests.create(
+			options.taskId,
+			options.phaseId,
+			options.draft,
+			options.cwd ?? process.cwd(),
+			options,
+		)
+		log(options.json ? JSON.stringify({ url }, null, 2) : url)
+	})
 
 export const pr = (args: readonly string[], cwd: string = process.cwd()) =>
 	Effect.gen(function* () {
@@ -24,8 +48,10 @@ export const pr = (args: readonly string[], cwd: string = process.cwd()) =>
 	})
 
 export const help = `
-Usage: agency pr [args...]
+Usage: agency pr create <task-id> [phase-id] [--draft] [--force] [--json]
+       agency pr [args...]
 
-Run gh pr unchanged, focusing the writable repository checkout when invoked
-from an Agency execution task or phase.
+Create records a pull request for an Agency execution unit. Other invocations
+run gh pr unchanged, focusing the writable repository checkout when invoked from
+an Agency execution task or phase.
 `

package/src/commands/sync.test.ts

@@ -0,0 +1,100 @@
+import { afterEach, beforeEach, describe, expect, test } from "bun:test"
+import { Effect } from "effect"
+import { mkdir } from "node:fs/promises"
+import { join } from "node:path"
+import { TaskService } from "../services/TaskService"
+import {
+	captureLogs,
+	cleanupTempDir,
+	createTempDir,
+	runTestEffect,
+} from "../test-utils"
+import { sync } from "./sync"
+
+const git = async (args: string[], cwd: string) => {
+	const process = Bun.spawn(["git", ...args], {
+		cwd,
+		stdout: "pipe",
+		stderr: "pipe",
+	})
+	await process.exited
+	if (process.exitCode !== 0) {
+		throw new Error(await new Response(process.stderr).text())
+	}
+}
+
+describe("sync command", () => {
+	let root: string
+
+	beforeEach(async () => {
+		root = await createTempDir()
+		const source = join(root, "source")
+		await mkdir(source)
+		await git(["init", "--initial-branch=main"], source)
+		await git(["config", "user.email", "test@example.com"], source)
+		await git(["config", "user.name", "Test"], source)
+		await Bun.write(join(source, "README.md"), "example\n")
+		await git(["add", "README.md"], source)
+		await git(["-c", "commit.gpgsign=false", "commit", "-m", "initial"], source)
+		await mkdir(join(root, "repos"))
+		await git(["clone", "--bare", source, join(root, "repos/agency")], root)
+		await Bun.write(join(root, "agency.json"), '{"version":2}\n')
+		await runTestEffect(
+			TaskService.pipe(
+				Effect.flatMap((service) =>
+					service.create(
+						{
+							id: "example",
+							ticketUrl: null,
+							repo: "agency",
+							branch: "task/example",
+							base: "main",
+						},
+						root,
+					),
+				),
+			),
+		)
+	})
+
+	afterEach(async () => cleanupTempDir(root))
+
+	test("applies safe reconciliation by default", async () => {
+		const logs = await captureLogs(() => runTestEffect(sync({ cwd: root })))
+
+		expect(
+			await Bun.file(join(root, "tasks/example/code/agency/README.md")).text(),
+		).toBe("example\n")
+		expect(logs).toContainEqual(
+			expect.stringContaining("Applied materialize-workspace 'task:example'"),
+		)
+		expect(() => JSON.parse(logs.join("\n"))).toThrow()
+	})
+
+	test("keeps explicit dry-run observational", async () => {
+		await runTestEffect(sync({ cwd: root, dryRun: true, silent: true }))
+
+		expect(
+			await Bun.file(
+				join(root, "tasks/example/code/agency/README.md"),
+			).exists(),
+		).toBe(false)
+	})
+
+	test("preserves structured output behind --json", async () => {
+		const logs = await captureLogs(() =>
+			runTestEffect(sync({ cwd: root, dryRun: true, json: true })),
+		)
+
+		expect(logs).toHaveLength(1)
+		expect(JSON.parse(logs[0]!)).toMatchObject({
+			mode: "dry-run",
+			changes: [
+				expect.objectContaining({
+					kind: "materialize-workspace",
+					status: "planned",
+				}),
+			],
+		})
+	})
+})

package/src/commands/sync.ts

@@ -4,7 +4,6 @@ import type { BaseCommandOptions } from "../utils/command"
 import { createLoggers } from "../utils/effect"
 
 interface SyncCommandOptions extends BaseCommandOptions {
-	readonly apply?: boolean
 	readonly dryRun?: boolean
 }
 
@@ -14,24 +13,62 @@ export const sync = (options: SyncCommandOptions = {}) =>
 		const { log } = createLoggers(options)
 		const result = yield* service.reconcile({
 			cwd: options.cwd,
-			apply: options.apply === true,
+			apply: options.dryRun !== true,
 		})
-		log(JSON.stringify(result, null, 2))
+		if (options.json) return log(JSON.stringify(result, null, 2))
+
+		for (const action of result.repositories.actions) {
+			log(
+				`${action.status === "applied" ? "Applied" : "Planned"} repository ${action.kind} '${action.alias}' from ${action.remote}`,
+			)
+		}
+		for (const change of result.changes) {
+			log(
+				`${change.status === "applied" ? "Applied" : "Planned"} ${change.kind} '${change.target}': ${change.message}`,
+			)
+		}
+		for (const warning of result.warnings) {
+			log(
+				`Warning '${warning.target}': ${warning.message}${warning.action ? `. ${warning.action}` : ""}`,
+			)
+		}
+		for (const issue of result.repositories.unresolved) {
+			log(
+				`Unresolved repository '${issue.alias}': ${issue.message}. ${issue.action}`,
+			)
+		}
+		for (const issue of result.unresolved) {
+			log(
+				`Unresolved '${issue.target}': ${issue.message}${issue.action ? `. ${issue.action}` : ""}`,
+			)
+		}
+		if (
+			result.repositories.actions.length === 0 &&
+			result.changes.length === 0 &&
+			result.warnings.length === 0 &&
+			result.repositories.unresolved.length === 0 &&
+			result.unresolved.length === 0
+		) {
+			log(
+				result.mode === "apply"
+					? "Workbase sync is current"
+					: "Workbase sync plan is current",
+			)
+		}
 	})
 
 export const help = `
-Usage: agency sync [--dry-run | --apply] [--json]
+Usage: agency sync [--dry-run] [--json]
 
 Compare portable repository declarations and execution state with local Git
 repositories, worktrees, branches, references, claims, and pull requests.
-Dry-run is the default.
+Safe reconciliation transitions are applied by default.
 
 Options:
   --dry-run                 Report planned safe transitions without changing state
-  --apply                   Apply safe reconciliation transitions
   --json                    Output one versioned machine result
 
-Apply may materialize declared repositories and unambiguous missing checkouts,
+Sync may materialize declared repositories and unambiguous missing checkouts,
 adopt legacy repositories with portable origins, release expired claims,
 record a uniquely matched PR, and mark merged work done. Dirty, stale, or
 conflicting checkouts are always left unresolved.

package/src/services/IntegrationService.test.ts

@@ -282,7 +282,7 @@ describe("IntegrationService", () => {
 		expect(body).toMatch(/completing\s+a refinement loop/)
 		expect(body).toContain("pausing or handing off")
 		expect(body).toContain("`agency finish`")
-		expect(body).toContain("`agency sync --apply`")
+		expect(body).toContain("`agency sync`")
 		expect(body).toContain("`--no-pull-request --summary <text>`")
 		expect(body).toContain("`TASK.md` or `PHASE.md`")
 		expect(body).toContain("PR state, current head, diff summary")

package/src/services/PhaseService.ts

@@ -654,7 +654,7 @@ export class PhaseService extends Effect.Service<PhaseService>()(
 						if (validStatus === "done") {
 							return yield* new PhaseError({
 								message:
-									"Work becomes done after its authoritative pull request is merged; run 'agency sync --apply', or explicitly complete a non-PR outcome with '--no-pull-request --summary <text>'",
+									"Work becomes done after its authoritative pull request is merged; run 'agency sync', or explicitly complete a non-PR outcome with '--no-pull-request --summary <text>'",
 							})
 						}
 						return yield* new PhaseError({

package/src/services/TaskService.ts

@@ -381,7 +381,7 @@ export class TaskService extends Effect.Service<TaskService>()("TaskService", {
 					if (validStatus === "done") {
 						return yield* new TaskError({
 							message:
-								"Work becomes done after its authoritative pull request is merged; run 'agency sync --apply', or explicitly complete a non-PR outcome with '--no-pull-request --summary <text>'",
+								"Work becomes done after its authoritative pull request is merged; run 'agency sync', or explicitly complete a non-PR outcome with '--no-pull-request --summary <text>'",
 						})
 					}
 					return yield* new TaskError({

package/src/workbase/AGENTS.md

@@ -59,8 +59,8 @@ to override readiness.
 - Do not run `agency work` from an active agent session unless the user
   explicitly asks to launch another agent.
 - Run `agency validate` before worktree or pull-request operations.
-- Create a pull request only with explicit user intent. Run `agency pr create`
-  from its execution unit, then use `agency sync --apply` to reconcile PR state.
+- Create a pull request only with explicit user intent. Run
+  `agency pr create <task> [phase]` so the URL is recorded durably.
 
 ## Execution
 
@@ -91,7 +91,7 @@ a refinement loop, or pausing or handing off completed implementation work):
 - Finish an active claim with the current revision via `agency finish`; a
   successful claim outcome leaves unmerged work `working`. For unclaimed work,
   keep the execution unit `working` through review and merge.
-- After merge, run `agency sync --apply` to reconcile the execution unit to
+- After merge, run `agency sync` to reconcile the execution unit to
   `done`.
 - For an approved non-PR outcome, finish an active claim or update unclaimed
   status with `--no-pull-request --summary <text>` and optional supporting URL.