@vaubaan/harness 1.3.0 → 1.4.0

package/dist/init.js

@@ -1,183 +1,217 @@
 // src/cli/init.ts
-import { existsSync as existsSync6, mkdirSync, writeFileSync as writeFileSync3 } from "fs";
-import { dirname as dirname3, join as join7, resolve as resolve3 } from "path";
-import { fileURLToPath } from "url";
-
-// src/loader.ts
-import { existsSync, readFileSync as readFileSync2 } from "fs";
-import { join } from "path";
-import fg from "fast-glob";
-import { z as z2 } from "zod";
-
-// src/parser/common.ts
-import { readFileSync } from "fs";
-import matter from "gray-matter";
-
-// src/parser/schemas.ts
-import { z } from "zod";
-
-// src/types.ts
-var AGENT_IDS = ["coding", "review", "merge", "planning"];
-var ENGINES = ["claude-code", "codex-cli", "opencode"];
-var CAPABILITIES = ["multi-step", "slash-command", "inline-exec"];
-var CAPABILITIES_MATRIX = {
-  "claude-code": ["multi-step", "slash-command", "inline-exec"],
-  "codex-cli": ["multi-step", "slash-command", "inline-exec"],
-  opencode: ["multi-step", "slash-command", "inline-exec"]
-};
-var DEGRADED_CAPABILITIES = {
-  "codex-cli": ["multi-step"]
-};
+import { existsSync as existsSync9, mkdirSync as mkdirSync2, rmSync, writeFileSync as writeFileSync4 } from "fs";
+import { dirname as dirname5, join as join11, resolve as resolve6 } from "path";
 
-// src/parser/schemas.ts
-var IdSchema = z.string().min(1).regex(/^[a-z][a-z0-9-]*$/, "id must be kebab-case (lowercase + digits + hyphens)");
-var SkillFrontmatterSchema = z.object({
-  id: IdSchema,
-  description: z.string().min(1),
-  engines: z.array(z.enum(ENGINES)).min(1).optional(),
-  requires: z.array(z.enum(CAPABILITIES)).optional(),
-  tags: z.array(z.string()).optional()
-}).strict();
-var CmdArgEnumSchema = z.object({
-  name: z.string().min(1),
-  type: z.literal("enum"),
-  values: z.array(z.string()).min(1),
-  default: z.string().optional()
-}).strict();
-var CmdArgStringSchema = z.object({
-  name: z.string().min(1),
-  type: z.literal("string"),
-  default: z.string().optional()
-}).strict();
-var CmdArgSchema = z.discriminatedUnion("type", [CmdArgEnumSchema, CmdArgStringSchema]);
-var CmdFrontmatterSchema = z.object({
-  id: IdSchema,
-  trigger: z.string().regex(/^\/[a-z][a-z0-9-]*$/, "trigger must be /kebab-case"),
-  invokes_skill: IdSchema,
-  args: z.array(CmdArgSchema).optional(),
-  description: z.string().min(1)
-}).strict();
-var AgentFrontmatterSchema = z.object({
-  id: z.enum(AGENT_IDS),
-  description: z.string().min(1)
-}).strict();
-var Schemas = {
-  Skill: SkillFrontmatterSchema,
-  Cmd: CmdFrontmatterSchema,
-  Agent: AgentFrontmatterSchema
-};
-var ParseError = class extends Error {
-  constructor(file, issues) {
-    const messages = issues.map((i) => `  - ${i.path.join(".") || "<root>"}: ${i.message}`).join("\n");
-    super(`Frontmatter validation failed for ${file}:
-${messages}`);
-    this.file = file;
-    this.issues = issues;
-    this.name = "ParseError";
+// src/cli/managed-paths.ts
+import { lstatSync, realpathSync, statSync } from "fs";
+import { basename, dirname, isAbsolute, join, resolve, win32 } from "path";
+var MANAGED_FILES = /* @__PURE__ */ new Set([
+  "AGENTS.md",
+  "CLAUDE.md",
+  ".mcp.json",
+  ".harness-manifest.json",
+  ".claude/settings.json",
+  ".codex/config.toml",
+  ".codex/hooks.json",
+  ".opencode/opencode.json",
+  ".opencode/mcp.json"
+]);
+var MANAGED_DIRECTORIES = [
+  ".claude/agents/",
+  ".claude/commands/",
+  ".claude/skills/",
+  ".codex/agents/",
+  ".codex/commands/",
+  ".codex/skills/",
+  ".agents/skills/",
+  ".opencode/agents/",
+  ".opencode/commands/",
+  ".opencode/skills/",
+  ".opencode/plugins/"
+];
+function canonicalTargetRoot(root) {
+  let ancestor = resolve(root);
+  const missing = [];
+  while (!lstatSync(ancestor, { throwIfNoEntry: false })) {
+    missing.unshift(basename(ancestor));
+    ancestor = dirname(ancestor);
   }
-  file;
-  issues;
-};
-
-// src/parser/common.ts
-function parseWithSchema(filePath, source, schema) {
-  const parsed = matter(source);
-  const result = schema.safeParse(parsed.data);
-  if (!result.success) {
-    throw new ParseError(filePath, result.error.issues);
+  const canonical = realpathSync(ancestor);
+  if (!statSync(canonical).isDirectory()) {
+    throw new Error(`harness target is not a directory: ${root}`);
   }
-  return {
-    meta: result.data,
-    body: parsed.content.trim(),
-    sourcePath: filePath
-  };
+  return join(canonical, ...missing);
 }
-
-// src/parser/agent.ts
-function parseAgent(filePath, source) {
-  return parseWithSchema(filePath, source, Schemas.Agent);
+function assertManagedLocation(path) {
+  const invalidSegment = path.split("/").some((part) => part === "" || part === "." || part === "..");
+  if (isAbsolute(path) || win32.isAbsolute(path) || path.includes("\\") || path.includes("\0") || invalidSegment) {
+    throw new Error(`unsafe harness path: ${path}`);
+  }
+  if (!MANAGED_FILES.has(path) && !MANAGED_DIRECTORIES.some((prefix) => path.startsWith(prefix))) {
+    throw new Error(`path is outside harness-managed locations: ${path}`);
+  }
 }
-
-// src/parser/cmd.ts
-function parseCmd(filePath, source) {
-  return parseWithSchema(filePath, source, Schemas.Cmd);
+function assertNoSymbolicComponents(root, path) {
+  const parts = path.split("/");
+  let current = root;
+  for (const [index, part] of parts.entries()) {
+    current = join(current, part);
+    const info = lstatSync(current, { throwIfNoEntry: false });
+    if (!info) return;
+    if (info.isSymbolicLink()) {
+      throw new Error(`symbolic link in harness path: ${path}`);
+    }
+    const isLeaf = index === parts.length - 1;
+    if (isLeaf ? !info.isFile() : !info.isDirectory()) {
+      throw new Error(`unexpected file type in harness path: ${path}`);
+    }
+  }
 }
-
-// src/parser/skill.ts
-function parseSkill(filePath, source) {
-  return parseWithSchema(filePath, source, Schemas.Skill);
+function assertManagedPaths(root, files) {
+  for (const path of files) assertManagedLocation(path);
+  const canonicalRoot2 = canonicalTargetRoot(root);
+  for (const path of files) assertNoSymbolicComponents(canonicalRoot2, path);
 }
 
-// src/util/yaml.ts
-import { parse as yamlParse } from "yaml";
-function parseYAML(source) {
-  return yamlParse(source);
-}
+// src/cli/manifest.ts
+import { createHash } from "crypto";
+import { chmodSync, existsSync as existsSync3, readFileSync as readFileSync3, writeFileSync } from "fs";
+import { join as join4 } from "path";
+import { z as z3 } from "zod";
 
-// src/loader.ts
-var DisableYamlSchema = z2.object({ disable: z2.array(z2.string()).optional() }).passthrough();
-function loadHarness(packageDir, opts = {}) {
-  const agentsDir = opts.agentsDir ?? join(packageDir, "agents");
-  const skillsDir = opts.skillsDir ?? join(packageDir, "skills");
-  const commandsDir = opts.commandsDir ?? join(packageDir, "commands");
-  const agentFiles = fg.sync("*.agent.md", { cwd: agentsDir, absolute: true });
-  const skillFiles = fg.sync("*.skill.md", { cwd: skillsDir, absolute: true });
-  const cmdFiles = fg.sync("*.cmd.md", { cwd: commandsDir, absolute: true });
-  return {
-    agents: agentFiles.map((f) => parseAgent(f, readFileSync2(f, "utf8"))),
-    skills: skillFiles.map((f) => parseSkill(f, readFileSync2(f, "utf8"))),
-    cmds: cmdFiles.map((f) => parseCmd(f, readFileSync2(f, "utf8")))
-  };
+// src/version.ts
+var VERSION = "1.4.0";
+
+// src/cli/opencode-config.ts
+import { existsSync, readFileSync } from "fs";
+import { join as join2 } from "path";
+import { isDeepStrictEqual } from "util";
+import { z } from "zod";
+var OPENCODE_CONFIG_PATH = ".opencode/opencode.json";
+var CLAUDE_MCP_PATH = ".mcp.json";
+var OPENCODE_SCHEMA = "https://opencode.ai/config.json";
+var ObjectSchema = z.record(z.unknown());
+var OPENCODE_TARGET = {
+  path: OPENCODE_CONFIG_PATH,
+  key: "mcp",
+  label: "OpenCode",
+  schema: OPENCODE_SCHEMA
+};
+var CLAUDE_TARGET = {
+  path: CLAUDE_MCP_PATH,
+  key: "mcpServers",
+  label: "Claude Code"
+};
+var OpenCodeConfigOwnershipSchema = z.object({
+  createdFile: z.boolean(),
+  addedMcp: z.boolean(),
+  addedSchema: z.boolean(),
+  entries: z.record(ObjectSchema)
+});
+function parseConfig(target, content) {
+  try {
+    const config = ObjectSchema.parse(JSON.parse(content));
+    if (Object.hasOwn(config, target.key)) ObjectSchema.parse(config[target.key]);
+    return config;
+  } catch {
+    throw new Error(`invalid ${target.path}: expected a JSON object with an MCP object`);
+  }
 }
-function loadProjectSkills(targetDir) {
-  const skillsDir = join(targetDir, "docs", "skills");
-  if (!existsSync(skillsDir)) return [];
-  const skillFiles = fg.sync("*.skill.md", { cwd: skillsDir, absolute: true });
-  return skillFiles.map((f) => parseSkill(f, readFileSync2(f, "utf8")));
+function removeOwnedEntries(target, config, ownership, warnings) {
+  if (Object.hasOwn(config, target.key)) {
+    const mcp = ObjectSchema.parse(config[target.key]);
+    for (const [id, installed] of Object.entries(ownership.entries)) {
+      if (!Object.hasOwn(mcp, id)) continue;
+      if (isDeepStrictEqual(mcp[id], installed)) delete mcp[id];
+      else warnings.push(`preserved modified ${target.label} MCP server: ${id}`);
+    }
+    config[target.key] = mcp;
+    if (ownership.addedMcp && Object.keys(mcp).length === 0)
+      Reflect.deleteProperty(config, target.key);
+  }
+  if (target.schema && ownership.addedSchema && config.$schema === target.schema)
+    Reflect.deleteProperty(config, "$schema");
 }
-function loadOverrides(worktreeDir) {
-  const overridesDir = join(worktreeDir, ".harness-overrides");
-  if (!existsSync(overridesDir)) return void 0;
-  const added = loadHarness(overridesDir, {
-    agentsDir: join(overridesDir, "agents"),
-    skillsDir: join(overridesDir, "skills"),
-    commandsDir: join(overridesDir, "commands")
-  });
-  const disablePath = join(overridesDir, "disable.yaml");
-  let disable = [];
-  if (existsSync(disablePath)) {
-    try {
-      const parsed = DisableYamlSchema.safeParse(parseYAML(readFileSync2(disablePath, "utf8")));
-      if (parsed.success && parsed.data.disable) {
-        disable = parsed.data.disable;
+function addMissingEntries(target, config, desired, createdFile, warnings) {
+  const requested = ObjectSchema.parse(parseConfig(target, desired.content)[target.key]);
+  const mcp = ObjectSchema.parse(config[target.key] ?? {});
+  const entries = {};
+  for (const [id, entry] of Object.entries(requested)) {
+    if (Object.hasOwn(mcp, id)) {
+      if (!isDeepStrictEqual(mcp[id], entry)) {
+        warnings.push(
+          `preserved existing ${target.label} MCP server instead of replacing it: ${id}`
+        );
       }
-    } catch {
+      continue;
     }
+    entries[id] = ObjectSchema.parse(entry);
+    mcp[id] = entry;
   }
-  return { add: added, disable };
+  if (Object.keys(entries).length === 0) return void 0;
+  const ownership = {
+    createdFile,
+    addedMcp: !Object.hasOwn(config, target.key),
+    addedSchema: target.schema !== void 0 && !Object.hasOwn(config, "$schema"),
+    entries
+  };
+  config[target.key] = mcp;
+  if (target.schema && ownership.addedSchema) config.$schema = target.schema;
+  return ownership;
 }
-
-// src/mcp.ts
-var MCP_SERVER_IDS = ["context7"];
-var MCP_SERVERS = {
-  context7: {
-    id: "context7",
-    description: "Upstash Context7 \u2014 fetches up-to-date library docs via resolve-library-id + get-library-docs.",
-    command: "npx",
-    args: ["-y", "@upstash/context7-mcp"]
+function planMcpJson(target, root, desired, previous) {
+  const warnings = [];
+  if (!desired && !previous) return { remove: false, warnings };
+  const path = join2(root, target.path);
+  const existed = existsSync(path);
+  if (!existed && !desired) return { remove: false, warnings };
+  const original = existed ? readFileSync(path, "utf8") : void 0;
+  const config = original === void 0 ? {} : parseConfig(target, original);
+  const before = structuredClone(config);
+  if (previous) removeOwnedEntries(target, config, previous, warnings);
+  const createdFile = !existed || previous?.createdFile === true;
+  const ownership = desired ? addMissingEntries(target, config, desired, createdFile, warnings) : void 0;
+  if (!ownership && createdFile && Object.keys(config).length === 0) {
+    return { remove: existed, warnings };
   }
-};
-function resolveMcpIds(requested) {
-  return requested.map((id) => {
-    if (!MCP_SERVER_IDS.includes(id)) {
-      throw new Error(`unknown MCP server: ${id} (expected one of ${MCP_SERVER_IDS.join(", ")})`);
-    }
-    return id;
-  });
+  return {
+    remove: false,
+    ownership,
+    warnings,
+    ...!existed || !isDeepStrictEqual(before, config) ? { write: { path: target.path, content: `${JSON.stringify(config, null, 2)}
+` } } : {}
+  };
+}
+function planOpenCodeConfig(root, desired, previous) {
+  return planMcpJson(OPENCODE_TARGET, root, desired, previous);
+}
+function planClaudeMcpConfig(root, desired, previous) {
+  return planMcpJson(CLAUDE_TARGET, root, desired, previous);
 }
 
+// src/cli/update-config.ts
+import { existsSync as existsSync2, readFileSync as readFileSync2 } from "fs";
+import { join as join3 } from "path";
+import { isDeepStrictEqual as isDeepStrictEqual2 } from "util";
+import { z as z2 } from "zod";
+
 // src/renderers/common.ts
 import { stringify as yamlStringify } from "yaml";
+
+// src/types.ts
+var AGENT_IDS = ["coding", "review", "merge", "planning"];
+var ENGINES = ["claude-code", "codex-cli", "opencode"];
+var CAPABILITIES = ["multi-step", "slash-command", "inline-exec"];
+var CAPABILITIES_MATRIX = {
+  "claude-code": ["multi-step", "slash-command", "inline-exec"],
+  "codex-cli": ["multi-step", "slash-command", "inline-exec"],
+  opencode: ["multi-step", "slash-command", "inline-exec"]
+};
+var DEGRADED_CAPABILITIES = {
+  "codex-cli": ["multi-step"]
+};
+
+// src/renderers/common.ts
 var STOP_HOOK_PACKAGE = "@vaubaan/harness";
 function checkSkillCapabilities(skill, engine) {
   const blockingWarnings = [];
@@ -543,18 +577,26 @@ ${body}` });
   renderStopHook() {
     const content = `import { spawnSync } from "node:child_process";
 
-export const HarnessStopHook = async ({ client, directory }) => ({
+// Runs the harness lint and returns the report to inject, or "" when the
+// turn may end.
+const lintReport = (directory, sessionID) => {
+  const r = spawnSync(
+    "npx",
+    ["-y", "${STOP_HOOK_PACKAGE}", "stop-hook", "--engine", "opencode", "--cwd", directory],
+    { input: JSON.stringify({ sessionID }), encoding: "utf-8" },
+  );
+  const report = (r.stderr ?? "").trim();
+  return r.status === 2 ? report : "";
+};
+
+// OpenCode 1.x entry point, exposed as server() below.
+const HarnessStopHook = async ({ client, directory }) => ({
   event: async ({ event }) => {
     if (event.type !== "session.idle") return;
     const sessionID = event.properties?.sessionID;
     if (!sessionID) return;
-    const r = spawnSync(
-      "npx",
-      ["-y", "${STOP_HOOK_PACKAGE}", "stop-hook", "--engine", "opencode", "--cwd", directory],
-      { input: JSON.stringify({ sessionID }), encoding: "utf-8" },
-    );
-    const report = (r.stderr ?? "").trim();
-    if (r.status !== 2 || report === "") return;
+    const report = lintReport(directory, sessionID);
+    if (report === "") return;
     // OpenCode defaults to its build agent when a prompt omits agent.
     // Preserve the last conversation persona, excluding compaction summaries.
     const history = await client.session.messages({ path: { id: sessionID } }).catch(() => undefined);
@@ -570,6 +612,31 @@ export const HarnessStopHook = async ({ client, directory }) => ({
     });
   },
 });
+
+// One default export for both majors: OpenCode 1.x calls server(),
+// OpenCode 2.x calls setup(). A V2 session keeps its agent, so the report
+// is sent without naming the persona.
+export default {
+  id: "vaubaan-harness-stop-hook",
+  server: HarnessStopHook,
+  setup(context) {
+    const directory = context.location.directory;
+    const controller = new AbortController();
+    const listen = async () => {
+      for await (const event of context.event.subscribe({ signal: controller.signal })) {
+        if (event.type !== "session.idle") continue;
+        if (event.location?.directory && event.location.directory !== directory) continue;
+        const sessionID = event.data?.sessionID;
+        if (!sessionID) continue;
+        const report = lintReport(directory, sessionID);
+        if (report === "") continue;
+        await context.session.prompt({ sessionID, text: report }).catch(() => undefined);
+      }
+    };
+    listen().catch(() => undefined);
+    return () => controller.abort();
+  },
+};
 `;
     return {
       files: [{ path: `${BASE3}/plugins/harness-stop-hook.ts`, content }],
@@ -588,7 +655,451 @@ function getRenderer(engine) {
   return RENDERERS[engine];
 }
 
-// src/render.ts
+// src/cli/update-config.ts
+var LEGACY_OPENCODE_CONFIG = ".opencode/mcp.json";
+var SHARED_CONFIG_PATHS = [
+  ".mcp.json",
+  ".codex/config.toml",
+  OPENCODE_CONFIG_PATH,
+  LEGACY_OPENCODE_CONFIG,
+  ".claude/settings.json",
+  ".codex/hooks.json"
+];
+var ObjectSchema2 = z2.record(z2.unknown());
+var HookEntrySchema = z2.object({ group: ObjectSchema2, hook: ObjectSchema2 });
+var HookConfigOwnershipSchema = z2.object({
+  createdFile: z2.boolean(),
+  addedHooks: z2.boolean(),
+  addedStop: z2.boolean(),
+  entries: z2.array(HookEntrySchema)
+});
+var HookConfigsOwnershipSchema = z2.object({
+  ".claude/settings.json": HookConfigOwnershipSchema.optional(),
+  ".codex/hooks.json": HookConfigOwnershipSchema.optional()
+}).strict();
+var HOOK_ENGINES = {
+  ".claude/settings.json": "claude-code",
+  ".codex/hooks.json": "codex-cli"
+};
+function parseObject(content, path) {
+  try {
+    return ObjectSchema2.parse(JSON.parse(content));
+  } catch {
+    throw new Error(`invalid shared configuration ${path}: expected a JSON object`);
+  }
+}
+function asObject(value) {
+  const parsed = ObjectSchema2.safeParse(value);
+  return parsed.success ? parsed.data : void 0;
+}
+function stopHooks(config, path) {
+  if (!Object.hasOwn(config, "hooks")) return [];
+  const hooks = asObject(config.hooks);
+  if (!hooks || Object.hasOwn(hooks, "Stop") && !Array.isArray(hooks.Stop)) {
+    throw new Error(`invalid shared configuration ${path}: expected hooks.Stop to be an array`);
+  }
+  return Array.isArray(hooks.Stop) ? hooks.Stop : [];
+}
+function groupMetadata(group) {
+  return Object.fromEntries(Object.entries(group).filter(([key]) => key !== "hooks"));
+}
+function sameEntry(left, right) {
+  return isDeepStrictEqual2(left.group, right.group) && isDeepStrictEqual2(left.hook, right.hook);
+}
+function appendEntry(entries, entry) {
+  if (!entries.some((existing) => sameEntry(existing, entry))) entries.push(entry);
+}
+function defaultStopGroup(engine) {
+  const file = getRenderer(engine).renderStopHook().files[0];
+  if (!file) throw new Error(`missing Stop hook renderer for ${engine}`);
+  const group = asObject(stopHooks(parseObject(file.content, file.path), file.path)[0]);
+  if (!group || !Array.isArray(group.hooks) || !asObject(group.hooks[0])) {
+    throw new Error(`invalid Stop hook renderer for ${engine}`);
+  }
+  return group;
+}
+function normalizeHarnessHooks(groups, expected, previous, claimExisting, warnings, path) {
+  const defaultHook = ObjectSchema2.parse(expected.hooks[0]);
+  const entries = [...previous?.entries ?? []];
+  let found = false;
+  const normalized = groups.map((value) => {
+    const group = asObject(value);
+    if (!group) return value;
+    const flat = group.type === "command" && group.command === defaultHook.command;
+    const hooks = flat ? [group] : Array.isArray(group.hooks) ? group.hooks : [];
+    const metadata = flat ? groupMetadata(expected) : groupMetadata(group);
+    for (const value2 of hooks) {
+      const hook = asObject(value2);
+      if (!hook || hook.type !== "command" || hook.command !== defaultHook.command) continue;
+      found = true;
+      const entry = { group: metadata, hook };
+      if (!claimExisting) continue;
+      if (previous && !previous.entries.some((old) => sameEntry(old, entry))) {
+        warnings.push(`preserved modified harness Stop hook: ${path}`);
+      } else {
+        appendEntry(entries, entry);
+      }
+    }
+    return flat && claimExisting ? { ...metadata, hooks: [group] } : value;
+  });
+  if (!found && !previous?.entries.length) {
+    normalized.push(expected);
+    appendEntry(entries, { group: groupMetadata(expected), hook: defaultHook });
+  } else if (!found) {
+    warnings.push(`preserved removed or modified harness Stop hook: ${path}`);
+  }
+  return { groups: normalized, entries };
+}
+function removeOwnedHooks(config, ownership, path, warnings) {
+  const groups = stopHooks(config, path);
+  const remaining = [];
+  const matched = /* @__PURE__ */ new Set();
+  for (const value of groups) {
+    const group = asObject(value);
+    if (!group || !Array.isArray(group.hooks)) {
+      remaining.push(value);
+      continue;
+    }
+    const metadata = groupMetadata(group);
+    const hooks2 = group.hooks.filter((value2) => {
+      const hook = asObject(value2);
+      const entry = hook && ownership.entries.find((old) => sameEntry(old, { group: metadata, hook }));
+      if (entry) matched.add(entry);
+      return !entry;
+    });
+    if (hooks2.length > 0 || hooks2.length === group.hooks.length) {
+      remaining.push({ ...group, hooks: hooks2 });
+    }
+  }
+  if (matched.size < ownership.entries.length) {
+    warnings.push(`preserved removed or modified harness Stop hook: ${path}`);
+  }
+  const hooks = asObject(config.hooks);
+  if (!hooks) return;
+  if (ownership.addedStop && remaining.length === 0) Reflect.deleteProperty(hooks, "Stop");
+  else if (Object.hasOwn(hooks, "Stop")) hooks.Stop = remaining;
+  if (ownership.addedHooks && Object.keys(hooks).length === 0)
+    Reflect.deleteProperty(config, "hooks");
+  else config.hooks = hooks;
+}
+function recordMutation(plan, path, before, after, createdFile) {
+  if (createdFile && Object.keys(after).length === 0) {
+    if (before) plan.removals.push(path);
+  } else if (!isDeepStrictEqual2(before, after)) {
+    plan.writes.push({ path, content: `${JSON.stringify(after, null, 2)}
+` });
+  }
+}
+function planHookConfigCleanup(root, ownership) {
+  const plan = { writes: [], removals: [], warnings: [] };
+  if (!ownership) return plan;
+  const validated = HookConfigsOwnershipSchema.parse(ownership);
+  assertManagedPaths(root, Object.keys(validated));
+  for (const path of Object.keys(HOOK_ENGINES)) {
+    const owned = validated[path];
+    if (!owned || !existsSync2(join3(root, path))) continue;
+    const before = parseObject(readFileSync2(join3(root, path), "utf8"), path);
+    const config = structuredClone(before);
+    removeOwnedHooks(config, owned, path, plan.warnings);
+    recordMutation(plan, path, before, config, owned.createdFile);
+  }
+  return plan;
+}
+function planActiveHook(root, path, previous, claimExisting, plan) {
+  assertManagedPaths(root, [path]);
+  const existed = existsSync2(join3(root, path));
+  if (!existed && previous?.entries.length) {
+    plan.warnings.push(`preserved removed harness Stop hook configuration: ${path}`);
+    return previous;
+  }
+  const before = existed ? parseObject(readFileSync2(join3(root, path), "utf8"), path) : void 0;
+  const config = structuredClone(before ?? {});
+  const groups = stopHooks(config, path);
+  const hooks = asObject(config.hooks) ?? {};
+  const normalized = normalizeHarnessHooks(
+    groups,
+    defaultStopGroup(HOOK_ENGINES[path]),
+    previous,
+    claimExisting,
+    plan.warnings,
+    path
+  );
+  const legacyWholeFile = !previous && claimExisting && existed;
+  const ownership = {
+    createdFile: !existed || previous?.createdFile === true || legacyWholeFile,
+    addedHooks: previous?.addedHooks ?? (legacyWholeFile || !Object.hasOwn(config, "hooks")),
+    addedStop: previous?.addedStop ?? (legacyWholeFile || !Object.hasOwn(hooks, "Stop")),
+    entries: normalized.entries
+  };
+  if (!isDeepStrictEqual2(groups, normalized.groups)) {
+    config.hooks = { ...hooks, Stop: normalized.groups };
+  }
+  recordMutation(plan, path, before, config, ownership.createdFile);
+  return ownership.entries.length > 0 ? ownership : void 0;
+}
+function planLegacyOpenCode(root, previous, plan) {
+  if (!previous.files.includes(LEGACY_OPENCODE_CONFIG)) return;
+  const legacyPath = join3(root, LEGACY_OPENCODE_CONFIG);
+  if (!existsSync2(legacyPath)) return;
+  assertManagedPaths(root, [LEGACY_OPENCODE_CONFIG, OPENCODE_CONFIG_PATH]);
+  const legacy = parseObject(readFileSync2(legacyPath, "utf8"), LEGACY_OPENCODE_CONFIG);
+  if (!asObject(legacy.mcp)) {
+    throw new Error(
+      `invalid shared configuration ${LEGACY_OPENCODE_CONFIG}: expected an MCP object`
+    );
+  }
+  const merged = planOpenCodeConfig(
+    root,
+    { path: OPENCODE_CONFIG_PATH, content: JSON.stringify(legacy) },
+    void 0
+  );
+  if (merged.write) plan.writes.push(merged.write);
+  plan.warnings.push(...merged.warnings);
+  if (merged.ownership) {
+    const old = previous.opencodeConfig;
+    plan.opencodeConfig = {
+      createdFile: merged.ownership.createdFile || old?.createdFile === true,
+      addedMcp: merged.ownership.addedMcp || old?.addedMcp === true,
+      addedSchema: merged.ownership.addedSchema || old?.addedSchema === true,
+      entries: { ...old?.entries, ...merged.ownership.entries }
+    };
+  }
+  plan.removals.push(LEGACY_OPENCODE_CONFIG);
+}
+function planUpdateConfigs(root, previous, hookEngines) {
+  const plan = {
+    writes: [],
+    removals: [],
+    ownedFiles: [],
+    warnings: [],
+    ...previous.opencodeConfig ? { opencodeConfig: previous.opencodeConfig } : {}
+  };
+  planLegacyOpenCode(root, previous, plan);
+  const hookConfigs = {};
+  for (const path of Object.keys(HOOK_ENGINES)) {
+    const owned = previous.hookConfigs?.[path];
+    if (hookEngines.includes(HOOK_ENGINES[path])) {
+      hookConfigs[path] = planActiveHook(
+        root,
+        path,
+        owned,
+        previous.files.includes(path) || Boolean(owned),
+        plan
+      );
+    } else if (owned) {
+      const cleanup = planHookConfigCleanup(root, { [path]: owned });
+      plan.writes.push(...cleanup.writes);
+      plan.removals.push(...cleanup.removals);
+      plan.warnings.push(...cleanup.warnings);
+    }
+  }
+  if (Object.values(hookConfigs).some(Boolean)) plan.hookConfigs = hookConfigs;
+  if (hookEngines.includes("opencode")) {
+    const plugin = getRenderer("opencode").renderStopHook();
+    plan.writes.push(...plugin.files);
+    plan.ownedFiles.push(...plugin.files.map((file) => file.path));
+    plan.warnings.push(...plugin.warnings);
+  }
+  return plan;
+}
+
+// src/cli/manifest.ts
+var MANIFEST_FILENAME = ".harness-manifest.json";
+var MANIFEST_VERSION = "6";
+var ManifestSchema = z3.object({
+  version: z3.enum(["4", "5", MANIFEST_VERSION]),
+  engines: z3.array(z3.string()),
+  renderedAt: z3.string(),
+  files: z3.array(z3.string()),
+  stopHookInstalled: z3.boolean().optional(),
+  stopHookEngines: z3.array(z3.string()).optional(),
+  opencodeConfig: OpenCodeConfigOwnershipSchema.optional(),
+  /** Entries the harness added to `.mcp.json` (Claude Code). */
+  mcpConfig: OpenCodeConfigOwnershipSchema.optional(),
+  hookConfigs: HookConfigsOwnershipSchema.optional(),
+  harnessVersion: z3.string().optional(),
+  overridesDir: z3.string().optional(),
+  fileHashes: z3.record(z3.string().regex(/^[a-f0-9]{64}$/)).optional(),
+  preservedFiles: z3.array(z3.string()).optional()
+});
+function manifestPath(targetDir) {
+  return join4(targetDir, MANIFEST_FILENAME);
+}
+function hashContent(content) {
+  return createHash("sha256").update(content).digest("hex");
+}
+function readManifest(targetDir) {
+  assertManagedPaths(targetDir, [MANIFEST_FILENAME]);
+  const path = manifestPath(targetDir);
+  if (!existsSync3(path)) return null;
+  const raw = JSON.parse(readFileSync3(path, "utf8"));
+  return ManifestSchema.parse(raw);
+}
+
+// src/cli/plan-render.ts
+import { existsSync as existsSync5 } from "fs";
+import { dirname as dirname2, join as join6, resolve as resolve2 } from "path";
+import { fileURLToPath } from "url";
+
+// src/loader.ts
+import { existsSync as existsSync4, readFileSync as readFileSync5 } from "fs";
+import { join as join5 } from "path";
+import fg from "fast-glob";
+import { z as z5 } from "zod";
+
+// src/parser/common.ts
+import { readFileSync as readFileSync4 } from "fs";
+import matter from "gray-matter";
+
+// src/parser/schemas.ts
+import { z as z4 } from "zod";
+var IdSchema = z4.string().min(1).regex(/^[a-z][a-z0-9-]*$/, "id must be kebab-case (lowercase + digits + hyphens)");
+var SkillFrontmatterSchema = z4.object({
+  id: IdSchema,
+  description: z4.string().min(1),
+  engines: z4.array(z4.enum(ENGINES)).min(1).optional(),
+  requires: z4.array(z4.enum(CAPABILITIES)).optional(),
+  tags: z4.array(z4.string()).optional()
+}).strict();
+var CmdArgEnumSchema = z4.object({
+  name: z4.string().min(1),
+  type: z4.literal("enum"),
+  values: z4.array(z4.string()).min(1),
+  default: z4.string().optional()
+}).strict();
+var CmdArgStringSchema = z4.object({
+  name: z4.string().min(1),
+  type: z4.literal("string"),
+  default: z4.string().optional()
+}).strict();
+var CmdArgSchema = z4.discriminatedUnion("type", [CmdArgEnumSchema, CmdArgStringSchema]);
+var CmdFrontmatterSchema = z4.object({
+  id: IdSchema,
+  trigger: z4.string().regex(/^\/[a-z][a-z0-9-]*$/, "trigger must be /kebab-case"),
+  invokes_skill: IdSchema,
+  args: z4.array(CmdArgSchema).optional(),
+  description: z4.string().min(1)
+}).strict();
+var AgentFrontmatterSchema = z4.object({
+  id: z4.enum(AGENT_IDS),
+  description: z4.string().min(1)
+}).strict();
+var Schemas = {
+  Skill: SkillFrontmatterSchema,
+  Cmd: CmdFrontmatterSchema,
+  Agent: AgentFrontmatterSchema
+};
+var ParseError = class extends Error {
+  constructor(file, issues) {
+    const messages = issues.map((i) => `  - ${i.path.join(".") || "<root>"}: ${i.message}`).join("\n");
+    super(`Frontmatter validation failed for ${file}:
+${messages}`);
+    this.file = file;
+    this.issues = issues;
+    this.name = "ParseError";
+  }
+  file;
+  issues;
+};
+
+// src/parser/common.ts
+function parseWithSchema(filePath, source, schema) {
+  const parsed = matter(source);
+  const result = schema.safeParse(parsed.data);
+  if (!result.success) {
+    throw new ParseError(filePath, result.error.issues);
+  }
+  return {
+    meta: result.data,
+    body: parsed.content.trim(),
+    sourcePath: filePath
+  };
+}
+
+// src/parser/agent.ts
+function parseAgent(filePath, source) {
+  return parseWithSchema(filePath, source, Schemas.Agent);
+}
+
+// src/parser/cmd.ts
+function parseCmd(filePath, source) {
+  return parseWithSchema(filePath, source, Schemas.Cmd);
+}
+
+// src/parser/skill.ts
+function parseSkill(filePath, source) {
+  return parseWithSchema(filePath, source, Schemas.Skill);
+}
+
+// src/util/yaml.ts
+import { parse as yamlParse } from "yaml";
+function parseYAML(source) {
+  return yamlParse(source);
+}
+
+// src/loader.ts
+var DisableYamlSchema = z5.object({ disable: z5.array(z5.string()).optional() }).passthrough();
+function loadHarness(packageDir, opts = {}) {
+  const agentsDir = opts.agentsDir ?? join5(packageDir, "agents");
+  const skillsDir = opts.skillsDir ?? join5(packageDir, "skills");
+  const commandsDir = opts.commandsDir ?? join5(packageDir, "commands");
+  const agentFiles = fg.sync("*.agent.md", { cwd: agentsDir, absolute: true });
+  const skillFiles = fg.sync("*.skill.md", { cwd: skillsDir, absolute: true });
+  const cmdFiles = fg.sync("*.cmd.md", { cwd: commandsDir, absolute: true });
+  return {
+    agents: agentFiles.map((f) => parseAgent(f, readFileSync5(f, "utf8"))),
+    skills: skillFiles.map((f) => parseSkill(f, readFileSync5(f, "utf8"))),
+    cmds: cmdFiles.map((f) => parseCmd(f, readFileSync5(f, "utf8")))
+  };
+}
+function loadProjectSkills(targetDir) {
+  const skillsDir = join5(targetDir, "docs", "skills");
+  if (!existsSync4(skillsDir)) return [];
+  const skillFiles = fg.sync("*.skill.md", { cwd: skillsDir, absolute: true });
+  return skillFiles.map((f) => parseSkill(f, readFileSync5(f, "utf8")));
+}
+function loadOverrides(worktreeDir) {
+  const overridesDir = join5(worktreeDir, ".harness-overrides");
+  if (!existsSync4(overridesDir)) return void 0;
+  const added = loadHarness(overridesDir, {
+    agentsDir: join5(overridesDir, "agents"),
+    skillsDir: join5(overridesDir, "skills"),
+    commandsDir: join5(overridesDir, "commands")
+  });
+  const disablePath = join5(overridesDir, "disable.yaml");
+  let disable = [];
+  if (existsSync4(disablePath)) {
+    try {
+      const parsed = DisableYamlSchema.safeParse(parseYAML(readFileSync5(disablePath, "utf8")));
+      if (parsed.success && parsed.data.disable) {
+        disable = parsed.data.disable;
+      }
+    } catch {
+    }
+  }
+  return { add: added, disable };
+}
+
+// src/mcp.ts
+var MCP_SERVER_IDS = ["context7"];
+var MCP_SERVERS = {
+  context7: {
+    id: "context7",
+    description: "Upstash Context7 \u2014 fetches up-to-date library docs via resolve-library-id + get-library-docs.",
+    command: "npx",
+    args: ["-y", "@upstash/context7-mcp"]
+  }
+};
+function resolveMcpIds(requested) {
+  return requested.map((id) => {
+    if (!MCP_SERVER_IDS.includes(id)) {
+      throw new Error(`unknown MCP server: ${id} (expected one of ${MCP_SERVER_IDS.join(", ")})`);
+    }
+    return id;
+  });
+}
+
+// src/render.ts
 var RenderError = class extends Error {
   constructor(message) {
     super(message);
@@ -688,320 +1199,470 @@ function render(input) {
   return { files, warnings };
 }
 
-// src/cli/managed-paths.ts
-import { lstatSync, realpathSync, statSync } from "fs";
-import { basename, dirname, isAbsolute, join as join2, resolve, win32 } from "path";
-var MANAGED_FILES = /* @__PURE__ */ new Set([
-  "AGENTS.md",
-  "CLAUDE.md",
+// src/cli/plan-render.ts
+var QUALITY_DOC_PATH = "docs/quality/code-quality.md";
+function resolveEngineList(requested) {
+  if (!requested) return [...ENGINES];
+  if (requested.length === 0) throw new Error("no engine selected");
+  const engines = requested.map((e) => {
+    if (!ENGINES.includes(e)) {
+      throw new Error(`unknown engine: ${e} (expected one of ${ENGINES.join(", ")})`);
+    }
+    return e;
+  });
+  return [...new Set(engines)];
+}
+function defaultPackageDir() {
+  const here = dirname2(fileURLToPath(import.meta.url));
+  if (existsSync5(join6(here, "agents"))) return here;
+  return resolve2(here, "..");
+}
+function planInit(args) {
+  const engines = resolveEngineList(args.engines);
+  const packageDir = args.packageDir ?? defaultPackageDir();
+  const harness = loadHarness(packageDir);
+  const overrides = args.overridesDir ? loadOverrides(args.overridesDir) : void 0;
+  const projectSkills = loadProjectSkills(args.targetDir);
+  const hasQualityDoc = existsSync5(join6(args.targetDir, QUALITY_DOC_PATH));
+  const mcpServers = args.mcpServers ? resolveMcpIds(args.mcpServers) : void 0;
+  const stopHookInstalled = args.withStopHook !== false;
+  const output = render({
+    harness,
+    engines,
+    overrides,
+    projectSkills,
+    hasQualityDoc,
+    mcpServers,
+    withStopHook: stopHookInstalled
+  });
+  return { engines, output, stopHookInstalled };
+}
+
+// src/cli/uninstall.ts
+import {
+  existsSync as existsSync6,
+  readFileSync as readFileSync6,
+  readdirSync,
+  rmdirSync,
+  unlinkSync,
+  writeFileSync as writeFileSync2
+} from "fs";
+import { dirname as dirname3, join as join7, relative, resolve as resolve3 } from "path";
+function pruneEmptyDirs(root, leaves) {
+  const candidates = /* @__PURE__ */ new Set();
+  for (const leaf of leaves) {
+    let cur = leaf;
+    while (cur !== root && cur.startsWith(`${root}/`)) {
+      candidates.add(cur);
+      cur = dirname3(cur);
+    }
+  }
+  const pruned = [];
+  const sorted = [...candidates].sort((a, b) => b.length - a.length);
+  for (const dir of sorted) {
+    if (!existsSync6(dir)) continue;
+    if (readdirSync(dir).length > 0) continue;
+    rmdirSync(dir);
+    pruned.push(relative(root, dir));
+  }
+  return pruned;
+}
+
+// src/cli/update-transaction.ts
+import { createHash as createHash2, randomUUID } from "crypto";
+import {
+  chmodSync as chmodSync2,
+  closeSync,
+  fsyncSync,
+  lstatSync as lstatSync2,
+  mkdirSync,
+  openSync,
+  readFileSync as readFileSync7,
+  readdirSync as readdirSync2,
+  realpathSync as realpathSync2,
+  rmdirSync as rmdirSync2,
+  unlinkSync as unlinkSync2,
+  writeFileSync as writeFileSync3
+} from "fs";
+import { homedir } from "os";
+import { basename as basename2, dirname as dirname4, isAbsolute as isAbsolute2, join as join8, relative as relative2, resolve as resolve4, sep } from "path";
+var MANIFEST_PATH = ".harness-manifest.json";
+var PRIVATE_FILES = /* @__PURE__ */ new Set([
+  MANIFEST_PATH,
   ".mcp.json",
-  ".harness-manifest.json",
-  ".claude/settings.json",
   ".codex/config.toml",
   ".codex/hooks.json",
+  ".claude/settings.json",
   ".opencode/opencode.json",
   ".opencode/mcp.json"
 ]);
-var MANAGED_DIRECTORIES = [
-  ".claude/agents/",
-  ".claude/commands/",
-  ".claude/skills/",
-  ".codex/agents/",
-  ".codex/commands/",
-  ".codex/skills/",
-  ".agents/skills/",
-  ".opencode/agents/",
-  ".opencode/commands/",
-  ".opencode/skills/",
-  ".opencode/plugins/"
-];
-function canonicalTargetRoot(root) {
-  let ancestor = resolve(root);
+function canonicalRoot(root) {
+  let ancestor = resolve4(root);
   const missing = [];
-  while (!lstatSync(ancestor, { throwIfNoEntry: false })) {
-    missing.unshift(basename(ancestor));
-    ancestor = dirname(ancestor);
-  }
-  const canonical = realpathSync(ancestor);
-  if (!statSync(canonical).isDirectory()) {
-    throw new Error(`harness target is not a directory: ${root}`);
+  while (!lstatSync2(ancestor, { throwIfNoEntry: false })) {
+    missing.unshift(basename2(ancestor));
+    ancestor = dirname4(ancestor);
   }
-  return join2(canonical, ...missing);
+  return join8(realpathSync2(ancestor), ...missing);
 }
-function assertManagedLocation(path) {
-  const invalidSegment = path.split("/").some((part) => part === "" || part === "." || part === "..");
-  if (isAbsolute(path) || win32.isAbsolute(path) || path.includes("\\") || path.includes("\0") || invalidSegment) {
-    throw new Error(`unsafe harness path: ${path}`);
+function contains(parent, child) {
+  const path = relative2(parent, child);
+  return path === "" || !isAbsolute2(path) && path !== ".." && !path.startsWith(`..${sep}`);
+}
+function assertBackupLocation(root, backup) {
+  if (contains(root, backup) || contains(backup, root)) {
+    throw new Error(`update backup must be outside the target project: ${backup}`);
   }
-  if (!MANAGED_FILES.has(path) && !MANAGED_DIRECTORIES.some((prefix) => path.startsWith(prefix))) {
-    throw new Error(`path is outside harness-managed locations: ${path}`);
+  const ancestors = [];
+  for (let path = backup; ; path = dirname4(path)) {
+    ancestors.unshift(path);
+    if (dirname4(path) === path) break;
   }
-}
-function assertNoSymbolicComponents(root, path) {
-  const parts = path.split("/");
-  let current = root;
-  for (const [index, part] of parts.entries()) {
-    current = join2(current, part);
-    const info = lstatSync(current, { throwIfNoEntry: false });
-    if (!info) return;
-    if (info.isSymbolicLink()) {
-      throw new Error(`symbolic link in harness path: ${path}`);
-    }
-    const isLeaf = index === parts.length - 1;
-    if (isLeaf ? !info.isFile() : !info.isDirectory()) {
-      throw new Error(`unexpected file type in harness path: ${path}`);
+  for (const path of ancestors) {
+    const info = lstatSync2(path, { throwIfNoEntry: false });
+    if (!info) continue;
+    if (info.isSymbolicLink() || !info.isDirectory()) {
+      throw new Error(`unsafe update backup directory: ${path}`);
     }
   }
+  if (lstatSync2(backup, { throwIfNoEntry: false })) {
+    throw new Error(`update backup directory already exists: ${backup}`);
+  }
 }
-function assertManagedPaths(root, files) {
-  for (const path of files) assertManagedLocation(path);
-  const canonicalRoot = canonicalTargetRoot(root);
-  for (const path of files) assertNoSymbolicComponents(canonicalRoot, path);
+function createDirectories(path, created, mode = 511) {
+  const missing = [];
+  for (let current = path; !lstatSync2(current, { throwIfNoEntry: false }); current = dirname4(current)) {
+    missing.unshift(current);
+  }
+  for (const directory of missing) {
+    mkdirSync(directory, { mode });
+    created.push(directory);
+  }
 }
-
-// src/cli/manifest.ts
-import { createHash } from "crypto";
-import { chmodSync, existsSync as existsSync4, readFileSync as readFileSync5, writeFileSync } from "fs";
-import { join as join5 } from "path";
-import { z as z5 } from "zod";
-
-// src/version.ts
-var VERSION = "1.3.0";
-
-// src/cli/opencode-config.ts
-import { existsSync as existsSync2, readFileSync as readFileSync3 } from "fs";
-import { join as join3 } from "path";
-import { isDeepStrictEqual } from "util";
-import { z as z3 } from "zod";
-var OPENCODE_CONFIG_PATH = ".opencode/opencode.json";
-var OPENCODE_SCHEMA = "https://opencode.ai/config.json";
-var ObjectSchema = z3.record(z3.unknown());
-var OpenCodeConfigOwnershipSchema = z3.object({
-  createdFile: z3.boolean(),
-  addedMcp: z3.boolean(),
-  addedSchema: z3.boolean(),
-  entries: z3.record(ObjectSchema)
-});
-function parseConfig(content) {
+function writeBackupFile(path, content) {
+  createDirectories(dirname4(path), [], 448);
+  const fd = openSync(path, "wx", 384);
   try {
-    const config = ObjectSchema.parse(JSON.parse(content));
-    if (Object.hasOwn(config, "mcp")) ObjectSchema.parse(config.mcp);
-    return config;
-  } catch {
-    throw new Error(`invalid ${OPENCODE_CONFIG_PATH}: expected a JSON object with an MCP object`);
+    writeFileSync3(fd, content);
+    fsyncSync(fd);
+  } finally {
+    closeSync(fd);
   }
 }
-function removeOwnedEntries(config, ownership, warnings) {
-  if (Object.hasOwn(config, "mcp")) {
-    const mcp = ObjectSchema.parse(config.mcp);
-    for (const [id, installed] of Object.entries(ownership.entries)) {
-      if (!Object.hasOwn(mcp, id)) continue;
-      if (isDeepStrictEqual(mcp[id], installed)) delete mcp[id];
-      else warnings.push(`preserved modified OpenCode MCP server: ${id}`);
+function saveSnapshot(root, paths, backup) {
+  const entries = [];
+  createDirectories(dirname4(backup), [], 448);
+  mkdirSync(backup, { mode: 448 });
+  for (const path of paths) {
+    const full = join8(root, path);
+    const info = lstatSync2(full, { throwIfNoEntry: false });
+    if (!info) {
+      entries.push({ path, exists: false });
+      continue;
     }
-    config.mcp = mcp;
-    if (ownership.addedMcp && Object.keys(mcp).length === 0) Reflect.deleteProperty(config, "mcp");
+    const content = readFileSync7(full);
+    writeBackupFile(join8(backup, "files", path), content);
+    entries.push({
+      path,
+      exists: true,
+      mode: info.mode & 4095,
+      sha256: createHash2("sha256").update(content).digest("hex")
+    });
   }
-  if (ownership.addedSchema && config.$schema === OPENCODE_SCHEMA)
-    Reflect.deleteProperty(config, "$schema");
+  writeBackupFile(
+    join8(backup, "snapshot.json"),
+    `${JSON.stringify({ version: 1, root, createdAt: (/* @__PURE__ */ new Date()).toISOString(), entries }, null, 2)}
+`
+  );
+  return entries;
 }
-function addMissingEntries(config, desired, createdFile, warnings) {
-  const requested = ObjectSchema.parse(parseConfig(desired.content).mcp);
-  const mcp = ObjectSchema.parse(config.mcp ?? {});
-  const entries = {};
-  for (const [id, entry] of Object.entries(requested)) {
-    if (Object.hasOwn(mcp, id)) {
-      if (!isDeepStrictEqual(mcp[id], entry)) {
-        warnings.push(`preserved existing OpenCode MCP server instead of replacing it: ${id}`);
+function errorMessage(error) {
+  return error instanceof Error ? error.message : String(error);
+}
+function rollback(root, backup, entries, touched, createdDirectories) {
+  const errors = [];
+  for (const path of [...touched].reverse()) {
+    try {
+      assertManagedPaths(root, [path]);
+      const entry = entries.get(path);
+      const full = join8(root, path);
+      const current = lstatSync2(full, { throwIfNoEntry: false });
+      if (!entry?.exists) {
+        if (current) unlinkSync2(full);
+        continue;
       }
-      continue;
+      const original = readFileSync7(join8(backup, "files", path));
+      if (!current || !readFileSync7(full).equals(original)) {
+        if (current) unlinkSync2(full);
+        writeFileSync3(full, original, { mode: 384 });
+      }
+      chmodSync2(full, entry.mode);
+    } catch (error) {
+      errors.push(`${path}: ${errorMessage(error)}`);
     }
-    entries[id] = ObjectSchema.parse(entry);
-    mcp[id] = entry;
   }
-  if (Object.keys(entries).length === 0) return void 0;
-  const ownership = {
-    createdFile,
-    addedMcp: !Object.hasOwn(config, "mcp"),
-    addedSchema: !Object.hasOwn(config, "$schema"),
-    entries
-  };
-  config.mcp = mcp;
-  if (ownership.addedSchema) config.$schema = OPENCODE_SCHEMA;
-  return ownership;
+  for (const directory of [...createdDirectories].reverse()) {
+    try {
+      if (readdirSync2(directory).length === 0) rmdirSync2(directory);
+    } catch (error) {
+      errors.push(`${directory}: ${errorMessage(error)}`);
+    }
+  }
+  return errors;
 }
-function planOpenCodeConfig(root, desired, previous) {
-  const warnings = [];
-  if (!desired && !previous) return { remove: false, warnings };
-  const path = join3(root, OPENCODE_CONFIG_PATH);
-  const existed = existsSync2(path);
-  if (!existed && !desired) return { remove: false, warnings };
-  const original = existed ? readFileSync3(path, "utf8") : void 0;
-  const config = original === void 0 ? {} : parseConfig(original);
-  const before = structuredClone(config);
-  if (previous) removeOwnedEntries(config, previous, warnings);
-  const createdFile = !existed || previous?.createdFile === true;
-  const ownership = desired ? addMissingEntries(config, desired, createdFile, warnings) : void 0;
-  if (!ownership && createdFile && Object.keys(config).length === 0) {
-    return { remove: existed, warnings };
+function applyUpdateTransaction(root, writes, removals, backupDir) {
+  const paths = [.../* @__PURE__ */ new Set([...removals, ...writes.map((file) => file.path)])];
+  assertManagedPaths(root, paths);
+  const target = canonicalRoot(root);
+  const backup = resolve4(
+    backupDir ?? join8(homedir(), ".local", "state", "vaubaan-harness", "backups", randomUUID())
+  );
+  assertBackupLocation(target, backup);
+  let snapshot;
+  try {
+    snapshot = saveSnapshot(target, paths, backup);
+  } catch (error) {
+    throw new Error(
+      `could not prepare update backup at ${backup}; project unchanged: ${errorMessage(error)}`,
+      { cause: error }
+    );
   }
-  return {
-    remove: false,
-    ownership,
-    warnings,
-    ...!existed || !isDeepStrictEqual(before, config) ? { write: { path: OPENCODE_CONFIG_PATH, content: `${JSON.stringify(config, null, 2)}
-` } } : {}
-  };
+  const entries = new Map(snapshot.map((entry) => [entry.path, entry]));
+  const touched = /* @__PURE__ */ new Set();
+  const createdDirectories = [];
+  try {
+    assertManagedPaths(target, paths);
+    for (const path of removals) {
+      if (!lstatSync2(join8(target, path), { throwIfNoEntry: false })) continue;
+      touched.add(path);
+      unlinkSync2(join8(target, path));
+    }
+    for (const file of writes) {
+      const full = join8(target, file.path);
+      createDirectories(dirname4(full), createdDirectories);
+      touched.add(file.path);
+      const entry = entries.get(file.path);
+      const mode = file.path === MANIFEST_PATH ? 384 : entry?.exists ? entry.mode : PRIVATE_FILES.has(file.path) ? 384 : 420;
+      if (entry?.exists && file.path === MANIFEST_PATH) chmodSync2(full, mode);
+      writeFileSync3(full, file.content, { mode });
+      if (entry?.exists) chmodSync2(full, mode);
+    }
+  } catch (error) {
+    const failures = rollback(target, backup, entries, touched, createdDirectories);
+    const restoration = failures.length > 0 ? `rollback errors: ${failures.join("; ")}` : "rollback completed";
+    throw new Error(`update failed; backup: ${backup}; ${restoration}: ${errorMessage(error)}`, {
+      cause: error
+    });
+  }
+  return { backupDir: backup };
 }
 
-// src/cli/update-config.ts
-import { existsSync as existsSync3, readFileSync as readFileSync4 } from "fs";
-import { join as join4 } from "path";
-import { isDeepStrictEqual as isDeepStrictEqual2 } from "util";
-import { z as z4 } from "zod";
-var ObjectSchema2 = z4.record(z4.unknown());
-var HookEntrySchema = z4.object({ group: ObjectSchema2, hook: ObjectSchema2 });
-var HookConfigOwnershipSchema = z4.object({
-  createdFile: z4.boolean(),
-  addedHooks: z4.boolean(),
-  addedStop: z4.boolean(),
-  entries: z4.array(HookEntrySchema)
-});
-var HookConfigsOwnershipSchema = z4.object({
-  ".claude/settings.json": HookConfigOwnershipSchema.optional(),
-  ".codex/hooks.json": HookConfigOwnershipSchema.optional()
-}).strict();
+// src/cli/update.ts
+import { existsSync as existsSync8, readFileSync as readFileSync9 } from "fs";
+import { join as join10, resolve as resolve5 } from "path";
+import { isDeepStrictEqual as isDeepStrictEqual3 } from "util";
 
-// src/cli/manifest.ts
-var MANIFEST_FILENAME = ".harness-manifest.json";
-var MANIFEST_VERSION = "6";
-var ManifestSchema = z5.object({
-  version: z5.enum(["4", "5", MANIFEST_VERSION]),
-  engines: z5.array(z5.string()),
-  renderedAt: z5.string(),
-  files: z5.array(z5.string()),
-  stopHookInstalled: z5.boolean().optional(),
-  stopHookEngines: z5.array(z5.string()).optional(),
-  opencodeConfig: OpenCodeConfigOwnershipSchema.optional(),
-  hookConfigs: HookConfigsOwnershipSchema.optional(),
-  harnessVersion: z5.string().optional(),
-  overridesDir: z5.string().optional(),
-  fileHashes: z5.record(z5.string().regex(/^[a-f0-9]{64}$/)).optional(),
-  preservedFiles: z5.array(z5.string()).optional()
+// src/cli/update-manifest.ts
+import { existsSync as existsSync7, readFileSync as readFileSync8 } from "fs";
+import { join as join9 } from "path";
+import { z as z6 } from "zod";
+var EngineSchema = z6.enum(ENGINES);
+var LegacySchema = z6.object({
+  version: z6.enum(["1", "2", "3"]),
+  engine: EngineSchema.optional(),
+  engines: z6.array(EngineSchema).nonempty().optional(),
+  renderedAt: z6.string(),
+  files: z6.array(z6.string())
 });
-function manifestPath(targetDir) {
-  return join5(targetDir, MANIFEST_FILENAME);
-}
-function writeManifest(targetDir, engines, files, extras = {}) {
-  assertManagedPaths(targetDir, [MANIFEST_FILENAME]);
-  const manifest = {
-    version: MANIFEST_VERSION,
-    harnessVersion: VERSION,
-    engines: [...engines].sort(),
-    renderedAt: (/* @__PURE__ */ new Date()).toISOString(),
-    files: [...files].sort(),
-    fileHashes: Object.fromEntries(
-      files.filter((file) => existsSync4(join5(targetDir, file))).sort().map((file) => [file, hashContent(readFileSync5(join5(targetDir, file)))])
-    ),
-    ...extras.overridesDir ? { overridesDir: extras.overridesDir } : {},
-    ...extras.preservedFiles ? { preservedFiles: extras.preservedFiles } : {},
-    ...extras.hookConfigs ? { hookConfigs: extras.hookConfigs } : {},
-    ...extras.opencodeConfig ? { opencodeConfig: extras.opencodeConfig } : {},
-    ...extras.stopHookInstalled !== void 0 ? { stopHookInstalled: extras.stopHookInstalled } : {},
-    ...extras.stopHookEngines !== void 0 ? { stopHookEngines: [...extras.stopHookEngines].sort() } : {}
-  };
-  const path = manifestPath(targetDir);
-  if (existsSync4(path)) chmodSync(path, 384);
-  writeFileSync(path, `${JSON.stringify(manifest, null, 2)}
-`, { mode: 384 });
-}
-function hashContent(content) {
-  return createHash("sha256").update(content).digest("hex");
+
+// src/cli/update.ts
+var CODEX_CONFIG_PATH = ".codex/config.toml";
+function currentContent(root, path) {
+  return existsSync8(join10(root, path)) ? readFileSync9(join10(root, path), "utf8") : void 0;
 }
-function readManifest(targetDir) {
-  assertManagedPaths(targetDir, [MANIFEST_FILENAME]);
-  const path = manifestPath(targetDir);
-  if (!existsSync4(path)) return null;
-  const raw = JSON.parse(readFileSync5(path, "utf8"));
-  return ManifestSchema.parse(raw);
+function ownedUnchanged(root, previous, path) {
+  const content = currentContent(root, path);
+  if (content === void 0 || !previous.files.includes(path)) return false;
+  const hash = previous.fileHashes?.[path];
+  return hash === void 0 || hash === hashContent(content);
 }
-
-// src/cli/uninstall.ts
-import { existsSync as existsSync5, readdirSync, rmdirSync, unlinkSync, writeFileSync as writeFileSync2 } from "fs";
-import { dirname as dirname2, join as join6, relative, resolve as resolve2 } from "path";
-function removeRenderedFiles(root, files) {
-  assertManagedPaths(root, files);
-  const filesRemoved = [];
-  const missing = [];
-  const dirsToConsider = /* @__PURE__ */ new Set();
-  for (const rel of files) {
-    const full = join6(root, rel);
-    if (existsSync5(full)) {
-      unlinkSync(full);
-      filesRemoved.push(rel);
-      dirsToConsider.add(dirname2(full));
-    } else {
-      missing.push(rel);
+function checkArtifactConflicts(root, previous, writes, removals) {
+  const desired = new Map(writes.map((file) => [file.path, file.content]));
+  const conflicts = [];
+  for (const path of [...desired.keys(), ...removals]) {
+    if (SHARED_CONFIG_PATHS.includes(path)) continue;
+    const content = currentContent(root, path);
+    if (content === void 0 || content === desired.get(path)) continue;
+    if (!previous.files.includes(path)) {
+      conflicts.push(`existing file outside harness manifest: ${path}`);
+      continue;
     }
+    const hash = previous.fileHashes?.[path];
+    if (hash && hash !== hashContent(content)) conflicts.push(`modified harness file: ${path}`);
+  }
+  if (conflicts.length) {
+    throw new Error(
+      `${conflicts.join("\n")}
+move their content to docs/ or .harness-overrides/, or keep them as yours with --preserve <path>`
+    );
   }
-  return { filesRemoved, dirsPruned: pruneEmptyDirs(root, dirsToConsider), missing };
 }
-function pruneEmptyDirs(root, leaves) {
-  const candidates = /* @__PURE__ */ new Set();
-  for (const leaf of leaves) {
-    let cur = leaf;
-    while (cur !== root && cur.startsWith(`${root}/`)) {
-      candidates.add(cur);
-      cur = dirname2(cur);
+function legacyMcpOwnership(root, previous) {
+  if (!ownedUnchanged(root, previous, CLAUDE_MCP_PATH)) return void 0;
+  try {
+    const servers = JSON.parse(currentContent(root, CLAUDE_MCP_PATH) ?? "").mcpServers;
+    if (!servers || typeof servers !== "object" || Array.isArray(servers)) return void 0;
+    return { createdFile: true, addedMcp: true, addedSchema: false, entries: servers };
+  } catch {
+    return void 0;
+  }
+}
+function planMcp(root, settings, rendered, pendingWrites) {
+  const { previous } = settings;
+  const plan = {
+    writes: [],
+    removals: [],
+    owned: [],
+    plannedOpenCode: false,
+    warnings: []
+  };
+  const claudeOwnership = previous.mcpConfig ?? legacyMcpOwnership(root, previous);
+  const codexOwned = ownedUnchanged(root, previous, CODEX_CONFIG_PATH);
+  if (settings.mcpServers === void 0) {
+    if (codexOwned) plan.owned.push(CODEX_CONFIG_PATH);
+    plan.mcpConfig = claudeOwnership;
+    return plan;
+  }
+  const desired = (path) => rendered.find((file) => file.path === path);
+  if (!pendingWrites.some((file) => file.path === OPENCODE_CONFIG_PATH)) {
+    plan.plannedOpenCode = true;
+    if (previous.files.includes(OPENCODE_CONFIG_PATH) && !previous.opencodeConfig) {
+      plan.warnings.push(`preserved legacy shared configuration: ${OPENCODE_CONFIG_PATH}`);
     }
+    const opencode = planOpenCodeConfig(
+      root,
+      desired(OPENCODE_CONFIG_PATH),
+      previous.opencodeConfig
+    );
+    if (opencode.write) plan.writes.push(opencode.write);
+    if (opencode.remove) plan.removals.push(OPENCODE_CONFIG_PATH);
+    plan.opencodeConfig = opencode.ownership;
+    plan.warnings.push(...opencode.warnings);
   }
-  const pruned = [];
-  const sorted = [...candidates].sort((a, b) => b.length - a.length);
-  for (const dir of sorted) {
-    if (!existsSync5(dir)) continue;
-    if (readdirSync(dir).length > 0) continue;
-    rmdirSync(dir);
-    pruned.push(relative(root, dir));
+  const claude = planClaudeMcpConfig(root, desired(CLAUDE_MCP_PATH), claudeOwnership);
+  if (claude.write) plan.writes.push(claude.write);
+  if (claude.remove) plan.removals.push(CLAUDE_MCP_PATH);
+  plan.mcpConfig = claude.ownership;
+  plan.warnings.push(...claude.warnings);
+  const codex = desired(CODEX_CONFIG_PATH);
+  const codexExists = existsSync8(join10(root, CODEX_CONFIG_PATH));
+  if (codex && (!codexExists || codexOwned)) {
+    plan.writes.push(codex);
+    plan.owned.push(CODEX_CONFIG_PATH);
+  } else if (codex) {
+    plan.warnings.push(
+      `left ${CODEX_CONFIG_PATH} unchanged; add this block to it to enable MCP in Codex:
+${codex.content.trimEnd()}`
+    );
+  } else if (codexOwned) {
+    plan.removals.push(CODEX_CONFIG_PATH);
   }
-  return pruned;
+  return plan;
 }
-
-// src/cli/init.ts
-var QUALITY_DOC_PATH = "docs/quality/code-quality.md";
-function resolveEngineList(requested) {
-  if (!requested || requested.length === 0) return [...ENGINES];
-  return requested.map((e) => {
-    if (!ENGINES.includes(e)) {
-      throw new Error(`unknown engine: ${e} (expected one of ${ENGINES.join(", ")})`);
+function planInstallation(args, settings) {
+  const root = resolve5(args.targetDir);
+  const { previous, engines, hookEngines } = settings;
+  const preserved = [
+    .../* @__PURE__ */ new Set([...previous.preservedFiles ?? [], ...args.preserveFiles ?? []])
+  ].sort();
+  if (preserved.includes(MANIFEST_FILENAME))
+    throw new Error("cannot preserve the harness manifest");
+  if (preserved.some((path) => SHARED_CONFIG_PATHS.includes(path))) {
+    throw new Error(
+      "--preserve applies to generated artifacts; shared configurations use entry-level preservation"
+    );
+  }
+  assertManagedPaths(root, [...previous.files, ...preserved, ...SHARED_CONFIG_PATHS]);
+  const requestedOverrides = args.overridesDir ?? previous.overridesDir;
+  const overridesDir = args.overridesDir ? resolve5(args.overridesDir) : previous.overridesDir ? resolve5(root, previous.overridesDir) : root;
+  if (requestedOverrides && !existsSync8(join10(overridesDir, ".harness-overrides"))) {
+    throw new Error(`recorded overrides are missing: ${overridesDir}/.harness-overrides`);
+  }
+  const hasOverrides = existsSync8(join10(overridesDir, ".harness-overrides"));
+  const disablePath = join10(overridesDir, ".harness-overrides", "disable.yaml");
+  if (existsSync8(disablePath)) {
+    try {
+      DisableYamlSchema.parse(parseYAML(readFileSync9(disablePath, "utf8")));
+    } catch {
+      throw new Error(`invalid override selection: ${disablePath}`);
     }
-    return e;
-  });
-}
-function defaultPackageDir() {
-  const here = dirname3(fileURLToPath(import.meta.url));
-  if (existsSync6(join7(here, "agents"))) return here;
-  return resolve3(here, "..");
-}
-function planInit(args) {
-  const engines = resolveEngineList(args.engines);
-  const packageDir = args.packageDir ?? defaultPackageDir();
-  const harness = loadHarness(packageDir);
-  const overrides = args.overridesDir ? loadOverrides(args.overridesDir) : void 0;
-  const projectSkills = loadProjectSkills(args.targetDir);
-  const hasQualityDoc = existsSync6(join7(args.targetDir, QUALITY_DOC_PATH));
-  const mcpServers = args.mcpServers ? resolveMcpIds(args.mcpServers) : void 0;
-  const stopHookInstalled = args.withStopHook !== false;
-  const output = render({
-    harness,
+  }
+  const rendered = planInit({
+    targetDir: root,
+    packageDir: args.packageDir,
     engines,
-    overrides,
-    projectSkills,
-    hasQualityDoc,
-    mcpServers,
-    withStopHook: stopHookInstalled
+    overridesDir: hasOverrides ? overridesDir : void 0,
+    mcpServers: settings.mcpServers,
+    withStopHook: false
   });
-  return { engines, output, stopHookInstalled };
+  const generated = rendered.output.files.filter(
+    (file) => !SHARED_CONFIG_PATHS.includes(file.path)
+  );
+  const config = planUpdateConfigs(root, previous, hookEngines);
+  const mcp = planMcp(root, settings, rendered.output.files, config.writes);
+  const output = [...generated, ...config.writes, ...mcp.writes].filter(
+    (file) => !preserved.includes(file.path)
+  );
+  const owned = [
+    .../* @__PURE__ */ new Set([...generated.map((file) => file.path), ...config.ownedFiles, ...mcp.owned])
+  ].filter((file) => !preserved.includes(file)).sort();
+  const removals = [
+    .../* @__PURE__ */ new Set([
+      ...previous.files.filter(
+        (file) => !owned.includes(file) && !SHARED_CONFIG_PATHS.includes(file)
+      ),
+      ...config.removals,
+      ...mcp.removals
+    ])
+  ].filter((file) => !preserved.includes(file));
+  assertManagedPaths(root, [...output.map((file) => file.path), ...removals]);
+  checkArtifactConflicts(root, previous, output, removals);
+  const hashes = Object.fromEntries(
+    owned.map((path) => {
+      const content = output.find((file) => file.path === path)?.content ?? currentContent(root, path);
+      if (content === void 0) throw new Error(`missing planned harness file: ${path}`);
+      return [path, hashContent(content)];
+    })
+  );
+  const opencodeConfig = mcp.plannedOpenCode ? mcp.opencodeConfig : config.opencodeConfig;
+  const manifest = {
+    version: MANIFEST_VERSION,
+    harnessVersion: VERSION,
+    engines: [...engines].sort(),
+    renderedAt: previous.renderedAt,
+    files: owned,
+    fileHashes: hashes,
+    stopHookInstalled: hookEngines.length > 0,
+    stopHookEngines: [...hookEngines].sort(),
+    ...hasOverrides ? { overridesDir: overridesDir === root ? "." : overridesDir } : {},
+    ...preserved.length ? { preservedFiles: preserved } : {},
+    ...opencodeConfig ? { opencodeConfig } : {},
+    ...mcp.mcpConfig ? { mcpConfig: mcp.mcpConfig } : {},
+    ...config.hookConfigs ? { hookConfigs: config.hookConfigs } : {}
+  };
+  const writes = output.filter((file) => currentContent(root, file.path) !== file.content);
+  const existingRemovals = removals.filter((path) => existsSync8(join10(root, path)));
+  if (writes.length || existingRemovals.length || !isDeepStrictEqual3(previous, manifest)) {
+    manifest.renderedAt = (/* @__PURE__ */ new Date()).toISOString();
+    writes.push({ path: MANIFEST_FILENAME, content: `${JSON.stringify(manifest, null, 2)}
+` });
+  }
+  const warnings = [...rendered.output.warnings, ...config.warnings, ...mcp.warnings];
+  if (preserved.length) warnings.push(`preserved user-owned artifacts: ${preserved.join(", ")}`);
+  return { writes, removals: existingRemovals, owned, manifest, warnings };
 }
+
+// src/cli/init.ts
 function writeFilesToTarget(files, targetDir) {
   assertManagedPaths(
     targetDir,
@@ -1009,43 +1670,57 @@ function writeFilesToTarget(files, targetDir) {
   );
   const written = [];
   for (const f of files) {
-    const full = join7(targetDir, f.path);
-    mkdirSync(dirname3(full), { recursive: true });
-    writeFileSync3(full, f.content);
+    const full = join11(targetDir, f.path);
+    mkdirSync2(dirname5(full), { recursive: true });
+    writeFileSync4(full, f.content);
     written.push(f.path);
   }
   return written;
 }
+function emptyManifest(engines) {
+  return { version: MANIFEST_VERSION, engines: [...engines], renderedAt: "", files: [] };
+}
 function initCommand(args) {
-  const { engines, output, stopHookInstalled } = planInit(args);
-  const previous = readManifest(args.targetDir);
-  assertManagedPaths(args.targetDir, [
-    MANIFEST_FILENAME,
-    ...previous?.files ?? [],
-    ...output.files.map((file) => file.path),
-    ...previous?.opencodeConfig ? [OPENCODE_CONFIG_PATH] : []
-  ]);
-  const desiredConfig = output.files.find((file) => file.path === OPENCODE_CONFIG_PATH);
-  const config = planOpenCodeConfig(args.targetDir, desiredConfig, previous?.opencodeConfig);
-  const next = new Set(output.files.map((f) => f.path));
-  const stale = (previous?.files ?? []).filter((f) => !next.has(f) && f !== OPENCODE_CONFIG_PATH);
-  if (config.remove) stale.push(OPENCODE_CONFIG_PATH);
-  const staleFilesRemoved = removeRenderedFiles(resolve3(args.targetDir), stale).filesRemoved;
-  const ownedFiles = output.files.filter((file) => file.path !== OPENCODE_CONFIG_PATH);
-  const filesWritten = writeFilesToTarget(ownedFiles, args.targetDir);
-  if (config.write) writeFilesToTarget([config.write], args.targetDir);
-  writeManifest(args.targetDir, engines, filesWritten, {
-    stopHookInstalled,
-    stopHookEngines: stopHookInstalled ? engines : void 0,
-    opencodeConfig: config.ownership,
-    overridesDir: args.overridesDir ? resolve3(args.overridesDir) === resolve3(args.targetDir) ? "." : resolve3(args.overridesDir) : void 0
-  });
-  if (config.write) filesWritten.push(OPENCODE_CONFIG_PATH);
-  const warnings = [...output.warnings, ...config.warnings];
-  if (previous?.files.includes(OPENCODE_CONFIG_PATH) && !previous.opencodeConfig) {
-    warnings.push(`preserved legacy shared configuration: ${OPENCODE_CONFIG_PATH}`);
+  const root = resolve6(args.targetDir);
+  const engines = resolveEngineList(args.engines);
+  const stopHookInstalled = args.withStopHook !== false;
+  const previous = readManifest(root) ?? emptyManifest(engines);
+  const plan = planInstallation(
+    {
+      targetDir: root,
+      packageDir: args.packageDir,
+      overridesDir: args.overridesDir,
+      preserveFiles: args.preserveFiles
+    },
+    {
+      previous,
+      sourceVersion: previous.version,
+      engines,
+      hookEngines: stopHookInstalled ? engines : [],
+      mcpServers: args.mcpServers ?? []
+    }
+  );
+  const touchedExisting = [...plan.writes.map((file) => file.path), ...plan.removals].some(
+    (path) => path !== MANIFEST_FILENAME && existsSync9(join11(root, path))
+  );
+  let backupDir;
+  if (plan.writes.length || plan.removals.length) {
+    backupDir = applyUpdateTransaction(root, plan.writes, plan.removals, args.backupDir).backupDir;
+    if (!touchedExisting && !args.backupDir) {
+      rmSync(backupDir, { recursive: true, force: true });
+      backupDir = void 0;
+    }
+    pruneEmptyDirs(root, new Set(plan.removals.map((path) => dirname5(join11(root, path)))));
   }
-  return { filesWritten, staleFilesRemoved, warnings, stopHookInstalled };
+  const sharedWritten = plan.writes.map((file) => file.path).filter((path) => SHARED_CONFIG_PATHS.includes(path) && !plan.owned.includes(path));
+  return {
+    filesWritten: [...plan.owned, ...sharedWritten],
+    staleFilesRemoved: plan.removals,
+    warnings: plan.warnings,
+    stopHookInstalled,
+    engines,
+    ...backupDir ? { backupDir } : {}
+  };
 }
 export {
   initCommand,