hatch3r 1.6.0 → 1.6.2

package/dist/cli/index.js

@@ -14,7 +14,7 @@ var HATCH3R_VERSION;
 var init_version = __esm({
   "src/version.ts"() {
     "use strict";
-    HATCH3R_VERSION = "1.6.0";
+    HATCH3R_VERSION = "1.6.2";
   }
 });
 
@@ -2181,7 +2181,9 @@ function createManifest(options) {
   if (options.defaultBranch) {
     manifest.board = createMinimalBoardConfig(owner, repo, options.defaultBranch);
   }
-  if (options.tools.some((t) => WORKTREE_CAPABLE_TOOLS.has(t))) {
+  const autoEnable = options.tools.some((t) => WORKTREE_CAPABLE_TOOLS.has(t));
+  const shouldEnable = options.worktreeEnabled ?? autoEnable;
+  if (shouldEnable) {
     manifest.worktree = { enabled: true };
   }
   return manifest;
@@ -2399,7 +2401,7 @@ var init_resolve2 = __esm({
 
 // src/adapters/canonical.ts
 import { readFile as readFile9, readdir as readdir6, lstat as lstat2 } from "fs/promises";
-import { join as join12 } from "path";
+import { join as join12, relative as relative3 } from "path";
 import { parse as parseYaml2 } from "yaml";
 function precedenceRank(value) {
   if (value && RULE_PRECEDENCE_VALUES.includes(value)) {
@@ -2414,6 +2416,16 @@ function sortByPrecedence(items) {
     return a.id.localeCompare(b.id);
   });
 }
+function filterUserFacing(files, expectedFrontmatterType, baseDir) {
+  return files.filter((file) => {
+    const rel = relative3(baseDir, file.sourcePath);
+    if (rel === "" || rel.startsWith("..")) return true;
+    if (/^[A-Za-z]:[\\/]/.test(rel)) return true;
+    if (rel.includes("/") || rel.includes("\\")) return false;
+    if (file.frontmatterType && file.frontmatterType !== expectedFrontmatterType) return false;
+    return true;
+  });
+}
 function classifyFsError(err) {
   const code = err?.code;
   if (code === "ENOENT") return "NOT_FOUND";
@@ -2460,6 +2472,7 @@ function parseFrontmatter(rawContent, typeMismatches) {
     type: "rule",
     description: ""
   };
+  let rawType;
   if (parsed && typeof parsed === "object") {
     const scalarFields = ["id", "type", "description"];
     for (const field of scalarFields) {
@@ -2467,6 +2480,7 @@ function parseFrontmatter(rawContent, typeMismatches) {
       if (raw === void 0) continue;
       if (typeof raw === "string") {
         metadata[field] = raw;
+        if (field === "type") rawType = raw;
       } else if (typeMismatches) {
         typeMismatches.push(
           `${field} field must be a string, got ${describeYamlType(raw)} (value: ${JSON.stringify(raw)})`
@@ -2502,7 +2516,7 @@ function parseFrontmatter(rawContent, typeMismatches) {
   }
   metadata.type = metadata.type ?? "rule";
   metadata.description = metadata.description ?? "";
-  return { metadata, content: content ?? "" };
+  return { metadata, content: content ?? "", rawType };
 }
 async function readSingleMd(fullPath, fileType, fallbackId) {
   let stats;
@@ -2533,11 +2547,19 @@ async function readSingleMd(fullPath, fileType, fallbackId) {
     const errorResult = makeErrorResult(fullPath, err, "YAML_PARSE_ERROR");
     return errorResult;
   }
-  const { metadata, content } = parsed;
+  const { metadata, content, rawType } = parsed;
   const id = metadata.id || metadata.name || fallbackId;
   const canonical = {
     id,
     type: fileType,
+    // Preserve the author-declared frontmatter `type` alongside the reader
+    // bucket so downstream filters (see `filterUserFacing`) can distinguish
+    // user-invocable commands/agents from companion content
+    // (`shared-context`, `reference`, `mode`) within the same directory.
+    // `rawType` is undefined when the author omitted `type:`, so files
+    // without an explicit declaration fall through the filter's
+    // back-compat path and are kept.
+    frontmatterType: rawType,
     description: metadata.description ?? "",
     scope: metadata.scope,
     model: metadata.model,
@@ -2959,7 +2981,7 @@ function resolveSelection(preset, projectType, teamSize, index, customSelections
           (item) => item.protected || !item.tags.includes("greenfield") || item.tags.some((t) => t !== "greenfield" && t !== "team" && t !== "solo")
         );
       }
-      if (teamSize === "solo") {
+      if (teamSize === "solo" && preset.id !== "full") {
         selected = selected.filter((item) => {
           if (item.protected) return true;
           if (!item.tags.includes("team") && !item.tags.includes("board")) return true;
@@ -4231,7 +4253,7 @@ var init_hooks = __esm({
 });
 
 // src/adapters/base.ts
-import { dirname as dirname7 } from "path";
+import { dirname as dirname7, join as join17 } from "path";
 function output(path, content, managedContent) {
   return { path, content, managedContent, action: "create" };
 }
@@ -4345,6 +4367,27 @@ var init_base = __esm({
         }
         return files;
       }
+      /**
+       * Read canonical commands or agents and filter to only those that should
+       * appear in a tool's user-facing command/agent picker. Wraps
+       * {@link readCanonicalFiles} + {@link filterUserFacing} and applies
+       * provenance tracking only to the surviving files, so filtered-out
+       * companion content does not pollute the adapter's source-file manifest.
+       *
+       * Filter rules are documented on {@link filterUserFacing}: files in
+       * support subdirectories (`commands/board/`, `agents/modes/`, etc.) and
+       * top-level files with a non-primary frontmatter `type:` (e.g.
+       * `shared-context`, `reference`, `mode`) are excluded.
+       */
+      async readUserFacingCanonicalFiles(agentsDir, type) {
+        const files = await readCanonicalFiles(agentsDir, type, this.warnings);
+        const expectedType = type === "commands" ? "command" : "agent";
+        const filtered = filterUserFacing(files, expectedType, join17(agentsDir, type));
+        for (const f of filtered) {
+          if (f.sourcePath) this._trackedSourceFiles.add(f.sourcePath);
+        }
+        return filtered;
+      }
       /**
        * Returns the raw bridge orchestration content (no surrounding headers).
        * Use this when the adapter needs custom formatting around the bridge content.
@@ -4401,7 +4444,7 @@ var init_base = __esm({
       async inlineAgents(ctx, formatModel) {
         if (!ctx.features.agents) return [];
         const lines = [];
-        const agents = await this.readTrackedCanonicalFiles(ctx.agentsDir, "agents");
+        const agents = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents");
         const minimal = this.isMinimal(ctx);
         for (const agent of agents) {
           const { content, skip, overrides, warnings } = await applyCustomization(ctx.projectRoot, agent);
@@ -4459,7 +4502,7 @@ ${wrapInManagedBlock(content)}`, content));
       async processCommandsRaw(ctx, pathFn) {
         if (!ctx.features.commands) return [];
         const results = [];
-        const commands = await this.readTrackedCanonicalFiles(ctx.agentsDir, "commands");
+        const commands = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "commands");
         for (const cmd of commands) {
           const { content, skip, warnings } = await applyCustomizationRaw(ctx.projectRoot, cmd);
           this.warnings.push(...warnings);
@@ -4561,7 +4604,7 @@ var init_agentsmd = __esm({
           sections.push("");
         }
         if (ctx.features.agents) {
-          const agents = await readCanonicalFiles(ctx.agentsDir, "agents", this.warnings);
+          const agents = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents");
           for (const agent of agents) {
             const { content, skip, overrides, warnings } = await applyCustomization(ctx.projectRoot, agent);
             this.warnings.push(...warnings);
@@ -4695,7 +4738,6 @@ var init_amazonq = __esm({
     init_types();
     init_managedBlocks();
     init_base();
-    init_canonical();
     init_customization();
     AmazonQAdapter = class extends BaseAdapter {
       name = "amazon-q";
@@ -4720,7 +4762,7 @@ var init_amazonq = __esm({
         const hooks = await this.readHooks(ctx);
         const descriptorHooks = this.buildDescriptorHooks(hooks);
         if (ctx.features.agents) {
-          const agents = await readCanonicalFiles(ctx.agentsDir, "agents", this.warnings);
+          const agents = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents");
           for (const agent of agents) {
             const { content, skip, overrides, warnings } = await applyCustomization(ctx.projectRoot, agent);
             this.warnings.push(...warnings);
@@ -5358,7 +5400,7 @@ ${content}`;
           }
         }
         if (ctx.features.agents) {
-          const agents = await readCanonicalFiles(ctx.agentsDir, "agents", this.warnings);
+          const agents = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents");
           for (const agent of agents) {
             const { content, skip, overrides, warnings } = await applyCustomization(ctx.projectRoot, agent);
             this.warnings.push(...warnings);
@@ -5509,7 +5551,7 @@ var init_cline = __esm({
         const results = [];
         const customModes = [];
         if (ctx.features.agents) {
-          const agents = await readCanonicalFiles(ctx.agentsDir, "agents", this.warnings);
+          const agents = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents");
           for (const agent of agents) {
             const { content, skip, overrides, warnings } = await applyCustomization(ctx.projectRoot, agent);
             this.warnings.push(...warnings);
@@ -5710,7 +5752,7 @@ var init_codex = __esm({
           }
         }
         if (ctx.features.agents) {
-          const agents = await readCanonicalFiles(ctx.agentsDir, "agents", this.warnings);
+          const agents = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents");
           for (const agent of agents) {
             const { content, skip, overrides, warnings } = await applyCustomization(ctx.projectRoot, agent);
             this.warnings.push(...warnings);
@@ -5791,11 +5833,11 @@ var init_codex = __esm({
 
 // src/detect/packageManager.ts
 import { access as access6 } from "fs/promises";
-import { join as join17 } from "path";
+import { join as join18 } from "path";
 async function detectPackageManager(rootDir) {
   for (const { file, name } of LOCK_FILE_MAP) {
     try {
-      await access6(join17(rootDir, file));
+      await access6(join18(rootDir, file));
       return { name, ...PM_INFO[name] };
     } catch (err) {
       if (err.code !== "ENOENT") throw err;
@@ -5927,7 +5969,7 @@ ${wrapInManagedBlock(body)}`,
           );
         }
         if (ctx.features.agents) {
-          const agents = await readCanonicalFiles(ctx.agentsDir, "agents", this.warnings);
+          const agents = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents");
           for (const agent of agents) {
             const { content, skip, overrides, warnings } = await applyCustomization(ctx.projectRoot, agent);
             this.warnings.push(...warnings);
@@ -6032,7 +6074,7 @@ var init_cursor = __esm({
           }
         }
         if (ctx.features.agents) {
-          const agents = await readCanonicalFiles(ctx.agentsDir, "agents", this.warnings);
+          const agents = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents");
           for (const agent of agents) {
             const { content, skip, overrides, warnings } = await applyCustomization(ctx.projectRoot, agent);
             this.warnings.push(...warnings);
@@ -6138,6 +6180,7 @@ New to this project's agent setup? Progress through these stages:
 });
 
 // src/adapters/gemini.ts
+import { join as join19 } from "path";
 function mapToGeminiEvent(event) {
   const mapping = {
     "pre-commit": "BeforeTool",
@@ -6208,7 +6251,8 @@ var init_gemini = __esm({
           ...await this.processSkillsRaw(ctx, (id) => `.gemini/skills/${toPrefixedId(id)}/SKILL.md`)
         );
         if (ctx.features.commands) {
-          const commands = await readCanonicalFiles(ctx.agentsDir, "commands", this.warnings);
+          const commandsRaw = await readCanonicalFiles(ctx.agentsDir, "commands", this.warnings);
+          const commands = filterUserFacing(commandsRaw, "command", join19(ctx.agentsDir, "commands"));
           for (const cmd of commands) {
             const { content, skip, overrides, warnings } = await applyCustomization(ctx.projectRoot, cmd);
             this.warnings.push(...warnings);
@@ -6242,7 +6286,7 @@ var init_goose = __esm({
     GooseAdapter = class extends BaseAdapter {
       name = "goose";
       async doGenerate(ctx) {
-        const agents = ctx.features.agents ? await readCanonicalFiles(ctx.agentsDir, "agents", this.warnings) : [];
+        const agents = ctx.features.agents ? await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents") : [];
         const lines = [
           ...await this.bridgeHeader(ctx),
           ...await this.inlineRules(ctx),
@@ -6521,7 +6565,7 @@ var init_opencode = __esm({
         }
         results.push(output("opencode.json", JSON.stringify(opencodeConfig, null, 2)));
         if (ctx.features.agents) {
-          const agents = await readCanonicalFiles(ctx.agentsDir, "agents", this.warnings);
+          const agents = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents");
           for (const agent of agents) {
             const { content, skip, overrides, warnings } = await applyCustomization(ctx.projectRoot, agent);
             this.warnings.push(...warnings);
@@ -6600,7 +6644,7 @@ var init_windsurf = __esm({
        */
       async windsurfAgentToolPolicies(ctx) {
         if (!ctx.features.agents) return [];
-        const agents = await readCanonicalFiles(ctx.agentsDir, "agents", this.warnings);
+        const agents = await this.readUserFacingCanonicalFiles(ctx.agentsDir, "agents");
         const rows = [];
         for (const agent of agents) {
           const { skip } = await applyCustomization(ctx.projectRoot, agent);
@@ -6892,7 +6936,7 @@ var init_adapters = __esm({
 // src/env/mcpEnv.ts
 import { readFile as readFile15 } from "fs/promises";
 import { existsSync } from "fs";
-import { join as join19 } from "path";
+import { join as join21 } from "path";
 function getSourceEnvMcpCommand() {
   return process.platform === "win32" ? SOURCE_POWERSHELL : SOURCE_POSIX;
 }
@@ -6962,7 +7006,7 @@ function parseEnvFile(content) {
   return result;
 }
 async function ensureGitignoreEntry(rootDir) {
-  const gitignorePath = join19(rootDir, ".gitignore");
+  const gitignorePath = join21(rootDir, ".gitignore");
   let content = "";
   try {
     content = await readFile15(gitignorePath, "utf-8");
@@ -6978,7 +7022,7 @@ async function ensureGitignoreEntry(rootDir) {
 `);
 }
 async function ensureEnvMcp(rootDir, servers) {
-  const envPath = join19(rootDir, ENV_MCP_FILE);
+  const envPath = join21(rootDir, ENV_MCP_FILE);
   const vars = collectRequiredEnvVars(servers);
   if (vars.length === 0) {
     return { action: "skipped", path: ENV_MCP_FILE, newVars: [] };
@@ -7016,11 +7060,11 @@ var init_mcpEnv = __esm({
 
 // src/cli/shared/paths.ts
 import { existsSync as existsSync2 } from "fs";
-import { dirname as dirname8, join as join20 } from "path";
+import { dirname as dirname8, join as join22 } from "path";
 function findPackageRoot(startDir) {
   let dir = startDir;
   while (dir !== dirname8(dir)) {
-    if (existsSync2(join20(dir, "package.json"))) return dir;
+    if (existsSync2(join22(dir, "package.json"))) return dir;
     dir = dirname8(dir);
   }
   return startDir;
@@ -7079,7 +7123,7 @@ var init_checkpoints = __esm({
 
 // src/merge/orphanCleanup.ts
 import { access as access10, readFile as readFile19, unlink as unlink3 } from "fs/promises";
-import { basename as basename3, dirname as dirname11, relative as relative4, resolve as resolve3 } from "path";
+import { basename as basename3, dirname as dirname11, relative as relative5, resolve as resolve3 } from "path";
 function isManagedOutputBasename(fileName) {
   return fileName.startsWith(HATCH3R_PREFIX) || NN_HATCH3R_PREFIX_RE2.test(fileName);
 }
@@ -7094,7 +7138,7 @@ function diffOrphanCandidates(previousPaths, currentPaths) {
 }
 function isPathInKnownAdapterRoot(relPath, rootDir) {
   const abs = resolve3(rootDir, relPath);
-  const rel = relative4(rootDir, abs);
+  const rel = relative5(rootDir, abs);
   if (rel.startsWith("..") || resolve3(rootDir, rel) !== abs) return false;
   if (rel === "" || rel === ".") return false;
   const posix4 = rel.split(/[\\/]/).join("/");
@@ -7814,7 +7858,7 @@ __export(update_exports, {
 import { appendFile, cp as cp4, mkdir as mkdir8, readFile as readFile20, readdir as readdir11, stat as stat6 } from "fs/promises";
 import { execFileSync as execFileSync4 } from "child_process";
 import { fileURLToPath as fileURLToPath3 } from "url";
-import { dirname as dirname12, join as join24 } from "path";
+import { dirname as dirname12, join as join26 } from "path";
 import chalk7 from "chalk";
 import inquirer5 from "inquirer";
 async function readFileOrNull(filePath) {
@@ -7826,7 +7870,7 @@ async function readFileOrNull(filePath) {
 }
 async function appendFailure(agentsDir, phase, error2, tool) {
   try {
-    const logPath = join24(agentsDir, FAILURE_LOG_FILE);
+    const logPath = join26(agentsDir, FAILURE_LOG_FILE);
     const entry = createFailureLogEntry(phase, error2, {
       tool,
       version: HATCH3R_VERSION
@@ -7855,8 +7899,8 @@ async function copyHatch3rFiles(srcDir, destDir, insideHatch3rDir = false, selec
     throw err;
   }
   for (const entry of entries) {
-    const srcPath = join24(srcDir, entry.name);
-    const destPath = join24(destDir, entry.name);
+    const srcPath = join26(srcDir, entry.name);
+    const destPath = join26(destDir, entry.name);
     if (entry.isDirectory()) {
       if (selectedIds && entry.name.startsWith(HATCH3R_PREFIX)) {
         if (!selectedIds.has(entry.name)) continue;
@@ -7868,7 +7912,7 @@ async function copyHatch3rFiles(srcDir, destDir, insideHatch3rDir = false, selec
         insideHatch3rDir || !entry.name.startsWith(HATCH3R_PREFIX),
         selectedIds
       );
-      copied.push(...subCopied.map((p) => join24(entry.name, p)));
+      copied.push(...subCopied.map((p) => join26(entry.name, p)));
     } else if (entry.name.startsWith(HATCH3R_PREFIX) || insideHatch3rDir || ALWAYS_COPY_FILES.has(entry.name)) {
       if (selectedIds && entry.name.startsWith(HATCH3R_PREFIX)) {
         const baseId = entry.name.replace(/\.(md|mdc)$/, "");
@@ -7919,7 +7963,7 @@ async function runPackageUpdate(rootDir, options = {}) {
 async function runRegenerate(rootDir, manifest, options = {}) {
   const offset = options.stepOffset ?? 0;
   const total = options.totalSteps ?? 3;
-  const agentsDir = join24(rootDir, AGENTS_DIR);
+  const agentsDir = join26(rootDir, AGENTS_DIR);
   const contentRoot = findPackageRoot(__dirname3);
   const s1 = createSpinner(step(offset + 1, total, "Updating canonical files..."));
   s1.start();
@@ -7932,18 +7976,18 @@ async function runRegenerate(rootDir, manifest, options = {}) {
   }
   const copied = [];
   for (const dir of CONTENT_DIRS) {
-    const srcDir = join24(contentRoot, dir);
+    const srcDir = join26(contentRoot, dir);
     try {
-      const dirCopied = await copyHatch3rFiles(srcDir, join24(agentsDir, dir), false, selectedIds);
-      copied.push(...dirCopied.map((p) => join24(dir, p)));
+      const dirCopied = await copyHatch3rFiles(srcDir, join26(agentsDir, dir), false, selectedIds);
+      copied.push(...dirCopied.map((p) => join26(dir, p)));
     } catch (err) {
       if (err.code !== "ENOENT") throw err;
     }
   }
   const canonicalAgentsMd = await generateCanonicalAgentsMd(agentsDir);
-  await safeWriteFile(join24(agentsDir, "AGENTS.md"), canonicalAgentsMd);
+  await safeWriteFile(join26(agentsDir, "AGENTS.md"), canonicalAgentsMd);
   const rootAgentsMd = await generateRootAgentsMd(agentsDir);
-  await safeWriteFile(join24(rootDir, "AGENTS.md"), rootAgentsMd.full, {
+  await safeWriteFile(join26(rootDir, "AGENTS.md"), rootAgentsMd.full, {
     managedContent: rootAgentsMd.inner
   });
   s1.succeed(step(offset + 1, total, `Updated ${copied.length} canonical files`));
@@ -7991,9 +8035,9 @@ async function runRegenerate(rootDir, manifest, options = {}) {
         const toolPaths = [];
         for (const out of outputs) {
           if (options.diff) {
-            diffBefore.set(out.path, await readFileOrNull(join24(rootDir, out.path)));
+            diffBefore.set(out.path, await readFileOrNull(join26(rootDir, out.path)));
           }
-          const fullPath = join24(rootDir, out.path);
+          const fullPath = join26(rootDir, out.path);
           if (out.managedContent) {
             await safeWriteFile(fullPath, out.content, {
               managedContent: out.managedContent
@@ -8004,7 +8048,7 @@ async function runRegenerate(rootDir, manifest, options = {}) {
           addManagedFile(manifest, out.path);
           toolPaths.push(out.path);
           if (options.diff) {
-            diffAfter.set(out.path, await readFileOrNull(join24(rootDir, out.path)));
+            diffAfter.set(out.path, await readFileOrNull(join26(rootDir, out.path)));
           }
         }
         newManagedByAdapter[tool] = toolPaths;
@@ -8065,7 +8109,7 @@ async function runRegenerate(rootDir, manifest, options = {}) {
     const wtContent = await generateWorktreeInclude(manifest, rootDir);
     const wtManaged = extractManagedContent(wtContent);
     await safeWriteFile(
-      join24(rootDir, WORKTREE_INCLUDE_FILE),
+      join26(rootDir, WORKTREE_INCLUDE_FILE),
       wtContent,
       { managedContent: wtManaged }
     );
@@ -8101,7 +8145,7 @@ async function runRegenerate(rootDir, manifest, options = {}) {
   };
 }
 async function runUpdateDryRun(rootDir, manifest, options = {}) {
-  const agentsDir = join24(rootDir, AGENTS_DIR);
+  const agentsDir = join26(rootDir, AGENTS_DIR);
   const contentRoot = findPackageRoot(__dirname3);
   let selectedIds;
   if (manifest.content) {
@@ -8112,9 +8156,9 @@ async function runUpdateDryRun(rootDir, manifest, options = {}) {
   }
   const canonicalCandidates = [];
   for (const dir of CONTENT_DIRS) {
-    const srcDir = join24(contentRoot, dir);
+    const srcDir = join26(contentRoot, dir);
     const entries = await enumerateHatch3rFiles(srcDir, false, selectedIds);
-    for (const rel of entries) canonicalCandidates.push(join24(dir, rel));
+    for (const rel of entries) canonicalCandidates.push(join26(dir, rel));
   }
   const adapterChanges = /* @__PURE__ */ new Map();
   for (const tool of manifest.tools) {
@@ -8128,7 +8172,7 @@ async function runUpdateDryRun(rootDir, manifest, options = {}) {
       }
       const outputs = generationResult.outputs ?? [];
       for (const out of outputs) {
-        const existing = await readFileOrNull(join24(rootDir, out.path));
+        const existing = await readFileOrNull(join26(rootDir, out.path));
         if (existing === null) bucket.added.push(out.path);
         else if (existing !== out.content) bucket.modified.push(out.path);
         else bucket.unchanged.push(out.path);
@@ -8168,7 +8212,7 @@ async function enumerateHatch3rFiles(srcDir, insideHatch3rDir, selectedIds) {
   }
   const out = [];
   for (const entry of entries) {
-    const srcPath = join24(srcDir, entry.name);
+    const srcPath = join26(srcDir, entry.name);
     if (entry.isDirectory()) {
       if (selectedIds && entry.name.startsWith(HATCH3R_PREFIX)) {
         if (!selectedIds.has(entry.name)) continue;
@@ -8178,7 +8222,7 @@ async function enumerateHatch3rFiles(srcDir, insideHatch3rDir, selectedIds) {
         insideHatch3rDir || !entry.name.startsWith(HATCH3R_PREFIX),
         selectedIds
       );
-      out.push(...sub.map((p) => join24(entry.name, p)));
+      out.push(...sub.map((p) => join26(entry.name, p)));
     } else if (entry.name.startsWith(HATCH3R_PREFIX) || insideHatch3rDir || ALWAYS_COPY_FILES.has(entry.name)) {
       if (selectedIds && entry.name.startsWith(HATCH3R_PREFIX)) {
         const baseId = entry.name.replace(/\.(md|mdc)$/, "");
@@ -8230,7 +8274,7 @@ async function updateCommand(_opts) {
   for (const notice of allNotices) {
     warn(notice);
   }
-  const agentsDir = join24(rootDir, AGENTS_DIR);
+  const agentsDir = join26(rootDir, AGENTS_DIR);
   const integrityResults = await verifyIntegrity(agentsDir);
   const modified = integrityResults.filter((r) => r.status === "modified");
   const missing = integrityResults.filter((r) => r.status === "missing");
@@ -8375,7 +8419,7 @@ var init_update = __esm({
         id: "content-selections-init",
         condition: async (manifest) => manifest.content === void 0,
         execute: async (manifest, rootDir, headless) => {
-          const agentsDir = join24(rootDir, AGENTS_DIR);
+          const agentsDir = join26(rootDir, AGENTS_DIR);
           const content = await buildSelectionsFromDisk(agentsDir);
           if (headless) {
             content.projectType = "brownfield";
@@ -8464,12 +8508,12 @@ var init_update = __esm({
       {
         id: "customize-yaml-size",
         condition: async (_manifest, rootDir) => {
-          const agentsDir = join24(rootDir, AGENTS_DIR);
+          const agentsDir = join26(rootDir, AGENTS_DIR);
           try {
             const entries = await readdir11(agentsDir, { recursive: true });
             for (const entry of entries) {
               if (typeof entry === "string" && entry.endsWith(".customize.yaml")) {
-                const s = await stat6(join24(agentsDir, entry));
+                const s = await stat6(join26(agentsDir, entry));
                 if (s.size > 10240) return true;
               }
             }
@@ -8480,12 +8524,12 @@ var init_update = __esm({
         },
         execute: async (manifest, rootDir, _headless) => {
           const notices = [];
-          const agentsDir = join24(rootDir, AGENTS_DIR);
+          const agentsDir = join26(rootDir, AGENTS_DIR);
           try {
             const entries = await readdir11(agentsDir, { recursive: true });
             for (const entry of entries) {
               if (typeof entry === "string" && entry.endsWith(".customize.yaml")) {
-                const s = await stat6(join24(agentsDir, entry));
+                const s = await stat6(join26(agentsDir, entry));
                 if (s.size > 10240) {
                   notices.push(`Large customize file detected: ${entry} (${Math.round(s.size / 1024)}KB) \u2014 consider splitting`);
                 }
@@ -8520,7 +8564,7 @@ var init_update = __esm({
           const notices = [];
           if (enabled) {
             const wtContent = await generateWorktreeInclude(updated, rootDir);
-            await safeWriteFile(join24(rootDir, WORKTREE_INCLUDE_FILE), wtContent, {
+            await safeWriteFile(join26(rootDir, WORKTREE_INCLUDE_FILE), wtContent, {
               appendIfNoBlock: true
             });
             notices.push("Worktree isolation enabled \u2014 .worktreeinclude generated");
@@ -9036,14 +9080,14 @@ init_worktree();
 init_types();
 import { access as access9, mkdir as mkdir7, readFile as readFile18 } from "fs/promises";
 import { fileURLToPath as fileURLToPath2 } from "url";
-import { basename as basename2, dirname as dirname10, join as join23 } from "path";
+import { basename as basename2, dirname as dirname10, join as join25 } from "path";
 import chalk5 from "chalk";
 import inquirer3 from "inquirer";
 
 // src/detect/repoAnalyzer.ts
 init_packageManager();
 import { access as access7, readFile as readFile14, readdir as readdir10 } from "fs/promises";
-import { join as join18 } from "path";
+import { join as join20 } from "path";
 async function analyzeRepo(rootDir) {
   const [languages, pm, isMonorepo, hasExistingAgents, existingTools, frameworks, linters, testFrameworks, ciProviders] = await Promise.all([
     detectLanguages(rootDir),
@@ -9094,7 +9138,7 @@ async function detectLanguages(rootDir) {
   };
   for (const [lang, files] of Object.entries(indicators)) {
     for (const file of files) {
-      if (await pathExists(join18(rootDir, file))) {
+      if (await pathExists(join20(rootDir, file))) {
         languages.push(lang);
         break;
       }
@@ -9114,13 +9158,13 @@ async function detectLanguages(rootDir) {
   return languages;
 }
 async function detectMonorepo(rootDir) {
-  if (await pathExists(join18(rootDir, "pnpm-workspace.yaml"))) return true;
-  if (await pathExists(join18(rootDir, "lerna.json"))) return true;
-  if (await pathExists(join18(rootDir, "nx.json"))) return true;
-  if (await pathExists(join18(rootDir, "turbo.json"))) return true;
-  if (await pathExists(join18(rootDir, "pants.toml"))) return true;
+  if (await pathExists(join20(rootDir, "pnpm-workspace.yaml"))) return true;
+  if (await pathExists(join20(rootDir, "lerna.json"))) return true;
+  if (await pathExists(join20(rootDir, "nx.json"))) return true;
+  if (await pathExists(join20(rootDir, "turbo.json"))) return true;
+  if (await pathExists(join20(rootDir, "pants.toml"))) return true;
   try {
-    const pkgJson = await readFile14(join18(rootDir, "package.json"), "utf-8");
+    const pkgJson = await readFile14(join20(rootDir, "package.json"), "utf-8");
     const pkg = JSON.parse(pkgJson);
     if (pkg.workspaces) return true;
   } catch (err) {
@@ -9130,11 +9174,11 @@ async function detectMonorepo(rootDir) {
   return false;
 }
 async function detectExistingAgents(rootDir) {
-  return pathExists(join18(rootDir, ".agents"));
+  return pathExists(join20(rootDir, ".agents"));
 }
 var TOOL_INDICATORS = [
   { tool: "cursor", paths: [".cursor"] },
-  { tool: "copilot", paths: [join18(".github", "copilot-instructions.md")] },
+  { tool: "copilot", paths: [join20(".github", "copilot-instructions.md")] },
   { tool: "claude", paths: ["CLAUDE.md", ".claude"] },
   { tool: "opencode", paths: ["opencode.json", "opencode.jsonc"] },
   { tool: "windsurf", paths: [".windsurfrules"] },
@@ -9153,7 +9197,7 @@ async function detectExistingTools(rootDir) {
   const results = await Promise.allSettled(
     TOOL_INDICATORS.map(async ({ tool, paths }) => {
       for (const p of paths) {
-        if (await pathExists(join18(rootDir, p))) return tool;
+        if (await pathExists(join20(rootDir, p))) return tool;
       }
       return null;
     })
@@ -9203,7 +9247,7 @@ async function detectFrameworks(rootDir) {
   const configResults = await Promise.allSettled(
     FRAMEWORK_CONFIG_INDICATORS.map(async ({ framework, configs }) => {
       for (const cfg of configs) {
-        if (await pathExists(join18(rootDir, cfg))) return framework;
+        if (await pathExists(join20(rootDir, cfg))) return framework;
       }
       return null;
     })
@@ -9214,7 +9258,7 @@ async function detectFrameworks(rootDir) {
     }
   }
   try {
-    const raw = await readFile14(join18(rootDir, "package.json"), "utf-8");
+    const raw = await readFile14(join20(rootDir, "package.json"), "utf-8");
     const pkg = JSON.parse(raw);
     const allDeps = {
       ...pkg.dependencies,
@@ -9232,7 +9276,7 @@ async function detectFrameworks(rootDir) {
   const nonJsResults = await Promise.allSettled(
     NON_JS_FRAMEWORK_INDICATORS.map(async ({ framework, configs }) => {
       for (const cfg of configs) {
-        if (await pathExists(join18(rootDir, cfg))) return framework;
+        if (await pathExists(join20(rootDir, cfg))) return framework;
       }
       return null;
     })
@@ -9268,7 +9312,7 @@ async function detectLinters(rootDir) {
   const results = await Promise.allSettled(
     LINTER_INDICATORS.map(async ({ name, configs }) => {
       for (const cfg of configs) {
-        if (await pathExists(join18(rootDir, cfg))) return name;
+        if (await pathExists(join20(rootDir, cfg))) return name;
       }
       return null;
     })
@@ -9300,7 +9344,7 @@ async function detectTestFrameworks(rootDir) {
   const results = await Promise.allSettled(
     TEST_FRAMEWORK_INDICATORS.map(async ({ name, configs }) => {
       for (const cfg of configs) {
-        if (await pathExists(join18(rootDir, cfg))) return name;
+        if (await pathExists(join20(rootDir, cfg))) return name;
       }
       return null;
     })
@@ -9329,7 +9373,7 @@ async function detectCIProviders(rootDir) {
   const results = await Promise.allSettled(
     CI_PROVIDER_INDICATORS.map(async ({ name, configs }) => {
       for (const cfg of configs) {
-        if (await pathExists(join18(rootDir, cfg))) return name;
+        if (await pathExists(join20(rootDir, cfg))) return name;
       }
       return null;
     })
@@ -9545,7 +9589,7 @@ init_types();
 init_version();
 init_safeWrite();
 import { readFile as readFile16 } from "fs/promises";
-import { join as join21, normalize as normalize2, isAbsolute as isAbsolute2 } from "path";
+import { join as join23, normalize as normalize2, isAbsolute as isAbsolute2 } from "path";
 function isUnsafeRepoPath(repoPath) {
   if (repoPath.includes("\0")) return true;
   if (isAbsolute2(repoPath)) return true;
@@ -9591,7 +9635,7 @@ function validateWorkspaceManifest(data) {
   return true;
 }
 async function readWorkspaceManifest(rootDir) {
-  const manifestPath = join21(rootDir, AGENTS_DIR, WORKSPACE_MANIFEST_FILE);
+  const manifestPath = join23(rootDir, AGENTS_DIR, WORKSPACE_MANIFEST_FILE);
   let raw;
   try {
     raw = await readFile16(manifestPath, "utf-8");
@@ -9621,7 +9665,7 @@ async function readWorkspaceManifest(rootDir) {
   return parsed;
 }
 async function writeWorkspaceManifest(rootDir, manifest) {
-  const manifestPath = join21(rootDir, AGENTS_DIR, WORKSPACE_MANIFEST_FILE);
+  const manifestPath = join23(rootDir, AGENTS_DIR, WORKSPACE_MANIFEST_FILE);
   await atomicWriteFile(manifestPath, JSON.stringify(manifest, null, 2) + "\n");
 }
 function createWorkspaceManifest(name, defaults, repos, syncStrategy = "manual") {
@@ -9647,7 +9691,7 @@ init_agentsContent();
 init_paths();
 import { createHash as createHash4 } from "crypto";
 import { mkdir as mkdir6, access as access8, readFile as readFile17 } from "fs/promises";
-import { join as join22, relative as relative3 } from "path";
+import { join as join24, relative as relative4 } from "path";
 import { fileURLToPath } from "url";
 import { dirname as dirname9 } from "path";
 init_mcpEnv();
@@ -9780,11 +9824,11 @@ async function estimateTokensForContent(contentIds, index) {
     for (const item of items) {
       try {
         if (item.type === "skill") {
-          const skillPath = join22(CONTENT_ROOT, item.relativePath, "SKILL.md");
+          const skillPath = join24(CONTENT_ROOT, item.relativePath, "SKILL.md");
           const content = await readFile17(skillPath, "utf-8");
           totalChars += content.length;
         } else {
-          const filePath = join22(CONTENT_ROOT, item.relativePath);
+          const filePath = join24(CONTENT_ROOT, item.relativePath);
           const content = await readFile17(filePath, "utf-8");
           totalChars += content.length;
         }
@@ -9804,7 +9848,7 @@ async function syncWorkspaceRepos(workspaceRoot, options = {}) {
   const protectedIds = new Set(
     index.items.filter((item) => item.protected).map((item) => item.id)
   );
-  const wsAgentsDir = join22(workspaceRoot, AGENTS_DIR);
+  const wsAgentsDir = join24(workspaceRoot, AGENTS_DIR);
   const integrityResults = await verifyIntegrity(wsAgentsDir);
   const tampered = integrityResults.filter(
     (r) => r.status === "modified" || r.status === "tampered"
@@ -9857,8 +9901,8 @@ async function syncWorkspaceRepos(workspaceRoot, options = {}) {
   return { repos: results };
 }
 async function syncSingleRepo(workspaceRoot, wsManifest, wsChecksum, repoEntry, index, protectedIds, options) {
-  const repoDir = join22(workspaceRoot, repoEntry.path);
-  const repoAgentsDir = join22(repoDir, AGENTS_DIR);
+  const repoDir = join24(workspaceRoot, repoEntry.path);
+  const repoAgentsDir = join24(repoDir, AGENTS_DIR);
   try {
     await access8(repoDir);
   } catch {
@@ -9900,7 +9944,7 @@ async function syncSingleRepo(workspaceRoot, wsManifest, wsChecksum, repoEntry,
     }
   }
   const canonicalAgentsMd = await generateCanonicalAgentsMd(repoAgentsDir);
-  await safeWriteFile(join22(repoAgentsDir, "AGENTS.md"), canonicalAgentsMd, { force: true });
+  await safeWriteFile(join24(repoAgentsDir, "AGENTS.md"), canonicalAgentsMd, { force: true });
   const repoInfo = await analyzeRepo(repoDir);
   let gitOwner = repoEntry.owner ?? "";
   let gitRepo = repoEntry.repo ?? "";
@@ -9932,7 +9976,7 @@ async function syncSingleRepo(workspaceRoot, wsManifest, wsChecksum, repoEntry,
     languages: repoInfo.languages
   });
   manifest.workspace = {
-    rootPath: relative3(repoDir, workspaceRoot),
+    rootPath: relative4(repoDir, workspaceRoot),
     lastSync: (/* @__PURE__ */ new Date()).toISOString(),
     syncVersion: HATCH3R_VERSION,
     workspaceChecksum: wsChecksum,
@@ -9944,7 +9988,7 @@ async function syncSingleRepo(workspaceRoot, wsManifest, wsChecksum, repoEntry,
   }
   await writeManifest(repoDir, manifest);
   const rootAgentsMd = await generateRootAgentsMd(repoAgentsDir);
-  await safeWriteFile(join22(repoDir, "AGENTS.md"), rootAgentsMd.full, {
+  await safeWriteFile(join24(repoDir, "AGENTS.md"), rootAgentsMd.full, {
     managedContent: rootAgentsMd.inner,
     appendIfNoBlock: true
   });
@@ -9958,7 +10002,7 @@ async function syncSingleRepo(workspaceRoot, wsManifest, wsChecksum, repoEntry,
         options.onWarn?.(w);
       }
       for (const out of outputs) {
-        await safeWriteFile(join22(repoDir, out.path), out.content, {
+        await safeWriteFile(join24(repoDir, out.path), out.content, {
           managedContent: out.managedContent,
           appendIfNoBlock: true
         });
@@ -10095,8 +10139,8 @@ async function runInit(options) {
   }
 }
 async function runInitInner(options) {
-  const { rootDir, platform, owner, repo, namespace, project, defaultBranch, tools, features, mcpServers, repoInfo, contentSelection } = options;
-  const agentsDir = join23(rootDir, AGENTS_DIR);
+  const { rootDir, platform, owner, repo, namespace, project, defaultBranch, tools, features, mcpServers, repoInfo, contentSelection, worktreeEnabled } = options;
+  const agentsDir = join25(rootDir, AGENTS_DIR);
   const totalSteps = 4;
   const s1 = createSpinner(step(1, totalSteps, "Creating canonical files..."));
   s1.start();
@@ -10114,8 +10158,8 @@ async function runInitInner(options) {
       }
     }
   }
-  await mkdir7(join23(agentsDir, "learnings"), { recursive: true });
-  const learningsReadmePath = join23(agentsDir, "learnings", "README.md");
+  await mkdir7(join25(agentsDir, "learnings"), { recursive: true });
+  const learningsReadmePath = join25(agentsDir, "learnings", "README.md");
   try {
     await access9(learningsReadmePath);
   } catch (err) {
@@ -10125,7 +10169,7 @@ async function runInitInner(options) {
       throw err;
     }
   }
-  const mcpPath = join23(agentsDir, "mcp", "mcp.json");
+  const mcpPath = join25(agentsDir, "mcp", "mcp.json");
   try {
     const mcpRaw = await readFile18(mcpPath, "utf-8");
     const mcpParsed = JSON.parse(mcpRaw);
@@ -10149,18 +10193,18 @@ async function runInitInner(options) {
     if (!isExpected) throw err;
   }
   const canonicalAgentsMd = await generateCanonicalAgentsMd(agentsDir);
-  await safeWriteFile(join23(agentsDir, "AGENTS.md"), canonicalAgentsMd, { force: true });
+  await safeWriteFile(join25(agentsDir, "AGENTS.md"), canonicalAgentsMd, { force: true });
   s1.succeed(step(1, totalSteps, `Canonical files created (${countSelectionItems(contentSelection)} items)`));
   const s2 = createSpinner(step(2, totalSteps, "Preparing manifest..."));
   s2.start();
-  const manifest = createManifest({ platform, owner, repo, namespace, project, defaultBranch, tools, features, mcpServers, content: contentSelection, languages: repoInfo.languages });
+  const manifest = createManifest({ platform, owner, repo, namespace, project, defaultBranch, tools, features, mcpServers, content: contentSelection, languages: repoInfo.languages, worktreeEnabled });
   s2.succeed(step(2, totalSteps, "Manifest prepared"));
   const s3 = createSpinner(
     step(3, totalSteps, `Generating ${tools.map((t) => TOOL_DISPLAY_NAMES[t] ?? t).join(", ")} output...`)
   );
   s3.start();
   const rootAgentsMd = await generateRootAgentsMd(agentsDir);
-  await safeWriteFile(join23(rootDir, "AGENTS.md"), rootAgentsMd.full, {
+  await safeWriteFile(join25(rootDir, "AGENTS.md"), rootAgentsMd.full, {
     managedContent: rootAgentsMd.inner,
     appendIfNoBlock: true
   });
@@ -10176,7 +10220,7 @@ async function runInitInner(options) {
       }
       const toolPaths = [];
       for (const out of outputs) {
-        await safeWriteFile(join23(rootDir, out.path), out.content, {
+        await safeWriteFile(join25(rootDir, out.path), out.content, {
           managedContent: out.managedContent,
           appendIfNoBlock: true
         });
@@ -10207,14 +10251,10 @@ async function runInitInner(options) {
       warn(w);
     }
   }
-  const hasWorktreeTool = tools.some((t) => WORKTREE_CAPABLE_TOOLS.has(t));
-  if (hasWorktreeTool) {
-    manifest.worktree = manifest.worktree ?? { enabled: true };
-  }
   if (manifest.worktree?.enabled) {
     const wtContent = await generateWorktreeInclude(manifest, rootDir);
     const wtManaged = extractManagedContent(wtContent);
-    await safeWriteFile(join23(rootDir, WORKTREE_INCLUDE_FILE), wtContent, {
+    await safeWriteFile(join25(rootDir, WORKTREE_INCLUDE_FILE), wtContent, {
       managedContent: wtManaged,
       appendIfNoBlock: true
     });
@@ -10274,7 +10314,7 @@ async function runInitInner(options) {
   printBox("Hatch complete", summaryLines, "success");
 }
 async function checkExisting(rootDir, skipPrompt, newSelection) {
-  const hatchJsonPath = join23(rootDir, AGENTS_DIR, "hatch.json");
+  const hatchJsonPath = join25(rootDir, AGENTS_DIR, "hatch.json");
   try {
     await access9(hatchJsonPath);
     if (!skipPrompt) {
@@ -10400,6 +10440,7 @@ async function initCommand(opts = {}) {
     } else {
       tools2 = DEFAULT_TOOLS;
     }
+    const worktreeEnabled2 = opts.worktree ?? tools2.some((t) => WORKTREE_CAPABLE_TOOLS.has(t));
     const features2 = { ...DEFAULT_FEATURES };
     const platformMcp = PLATFORM_MCP_SERVER[platform2];
     const mcpServers2 = features2.mcp ? Array.from(/* @__PURE__ */ new Set([platformMcp, ...DEFAULT_MCP.filter((s) => s !== "github")])) : [];
@@ -10418,7 +10459,7 @@ async function initCommand(opts = {}) {
     }
     warnBoardPrerequisites(contentSelection2);
     await checkExisting(rootDir, true, contentSelection2);
-    await runInit({ rootDir, platform: platform2, owner: owner2, repo: repo2, namespace: namespace2, project: project2, defaultBranch: defaultBranch2, tools: tools2, features: features2, mcpServers: mcpServers2, repoInfo, contentSelection: contentSelection2 });
+    await runInit({ rootDir, platform: platform2, owner: owner2, repo: repo2, namespace: namespace2, project: project2, defaultBranch: defaultBranch2, tools: tools2, features: features2, mcpServers: mcpServers2, repoInfo, contentSelection: contentSelection2, worktreeEnabled: worktreeEnabled2 });
     return;
   }
   console.log();
@@ -10571,6 +10612,21 @@ async function initCommand(opts = {}) {
     }
   ]);
   const tools = toolAnswers.tools.length > 0 ? toolAnswers.tools : DEFAULT_TOOLS;
+  const hasWorktreeTool = tools.some((t) => WORKTREE_CAPABLE_TOOLS.has(t));
+  let worktreeEnabled;
+  if (opts.worktree !== void 0) {
+    worktreeEnabled = opts.worktree;
+  } else if (hasWorktreeTool) {
+    const wtAnswer = await inquirer3.prompt([{
+      type: "confirm",
+      name: "enabled",
+      message: "Enable worktree file isolation (for parallel agent sessions)?",
+      default: true
+    }]);
+    worktreeEnabled = wtAnswer.enabled;
+  } else {
+    worktreeEnabled = false;
+  }
   const secretNotes = tools.map((t) => TOOL_SECRET_NOTES[t]).filter(Boolean);
   if (secretNotes.length > 0) {
     info(chalk5.dim("MCP secret loading by tool:"));
@@ -10621,7 +10677,7 @@ async function initCommand(opts = {}) {
   }
   warnBoardPrerequisites(contentSelection);
   await checkExisting(rootDir, false, contentSelection);
-  await runInit({ rootDir, platform, owner, repo, namespace, project, defaultBranch, tools, features, mcpServers, repoInfo, contentSelection });
+  await runInit({ rootDir, platform, owner, repo, namespace, project, defaultBranch, tools, features, mcpServers, repoInfo, contentSelection, worktreeEnabled });
 }
 async function runWorkspaceInit(rootDir, detectedRepos, repoInfo, opts) {
   const headless = !!opts.yes;
@@ -10649,7 +10705,7 @@ async function runWorkspaceInit(rootDir, detectedRepos, repoInfo, opts) {
   }
   const enriched = detectedRepos.map((r) => ({
     ...r,
-    ...detectRepoGitIdentity(join23(rootDir, r.path))
+    ...detectRepoGitIdentity(join25(rootDir, r.path))
   }));
   wsSpinner.succeed(`Workspace: ${detectedRepos.length} repo(s) detected`);
   console.log();
@@ -10706,8 +10762,10 @@ async function runWorkspaceInit(rootDir, detectedRepos, repoInfo, opts) {
   let features;
   let mcpServers;
   let contentSelection;
+  let worktreeEnabled;
   if (headless) {
     tools = resolveToolsFromOpts(opts.tools, repoInfo);
+    worktreeEnabled = opts.worktree ?? tools.some((t) => WORKTREE_CAPABLE_TOOLS.has(t));
     features = { ...DEFAULT_FEATURES };
     const platformMcp = PLATFORM_MCP_SERVER[platform];
     mcpServers = features.mcp ? Array.from(/* @__PURE__ */ new Set([platformMcp, ...DEFAULT_MCP.filter((s) => s !== "github")])) : [];
@@ -10803,6 +10861,20 @@ async function runWorkspaceInit(rootDir, detectedRepos, repoInfo, opts) {
       }
     ]);
     tools = toolAnswers.tools.length > 0 ? toolAnswers.tools : DEFAULT_TOOLS;
+    const wsHasWorktreeTool = tools.some((t) => WORKTREE_CAPABLE_TOOLS.has(t));
+    if (opts.worktree !== void 0) {
+      worktreeEnabled = opts.worktree;
+    } else if (wsHasWorktreeTool) {
+      const wsWtAnswer = await inquirer3.prompt([{
+        type: "confirm",
+        name: "enabled",
+        message: "Enable worktree file isolation (for parallel agent sessions)?",
+        default: true
+      }]);
+      worktreeEnabled = wsWtAnswer.enabled;
+    } else {
+      worktreeEnabled = false;
+    }
     const wsSecretNotes = tools.map((t) => TOOL_SECRET_NOTES[t]).filter(Boolean);
     if (wsSecretNotes.length > 0) {
       info(chalk5.dim("MCP secret loading by tool:"));
@@ -10866,7 +10938,8 @@ async function runWorkspaceInit(rootDir, detectedRepos, repoInfo, opts) {
     features,
     mcpServers,
     repoInfo,
-    contentSelection
+    contentSelection,
+    worktreeEnabled
   });
   let repoEntries;
   if (headless) {
@@ -10995,7 +11068,8 @@ function captureConfig(manifest) {
       projectType: "brownfield",
       teamSize: "solo",
       items: { agents: [], skills: [], rules: [], commands: [], prompts: [], hooks: [], githubAgents: [] }
-    }
+    },
+    worktreeEnabled: manifest.worktree?.enabled ?? false
   };
 }
 function printInventory(inventory) {
@@ -11130,7 +11204,8 @@ async function cleanCommand(opts = {}) {
           features: config.features,
           mcpServers: config.mcpServers,
           repoInfo,
-          contentSelection: config.contentSelection
+          contentSelection: config.contentSelection,
+          worktreeEnabled: config.worktreeEnabled
         };
         await runInit(initOpts);
         if (learningsBackup) {
@@ -11191,7 +11266,7 @@ init_archive();
 init_paths();
 import { fileURLToPath as fileURLToPath4 } from "url";
 import { readFile as readFile21 } from "fs/promises";
-import { dirname as dirname13, join as join25 } from "path";
+import { dirname as dirname13, join as join27 } from "path";
 import chalk8 from "chalk";
 import inquirer6 from "inquirer";
 init_content();
@@ -11426,7 +11501,7 @@ async function configCommand() {
     );
     console.log();
     const contentRoot = findPackageRoot(__dirname4);
-    const agentsDir = join25(rootDir, AGENTS_DIR);
+    const agentsDir = join27(rootDir, AGENTS_DIR);
     const index = await buildContentIndex(contentRoot);
     const previousContent = manifest.content;
     const { projectType, teamSize } = manifest.content;
@@ -11480,7 +11555,7 @@ async function configCommand() {
           const keepItem = index.byId.get(keepId);
           if (!keepItem) continue;
           try {
-            const filePath = keepItem.type === "skill" ? join25(agentsDir, keepItem.relativePath, "SKILL.md") : join25(agentsDir, keepItem.relativePath);
+            const filePath = keepItem.type === "skill" ? join27(agentsDir, keepItem.relativePath, "SKILL.md") : join27(agentsDir, keepItem.relativePath);
             const content = await readFile21(filePath, "utf-8");
             const refs = extractContentReferences(content);
             if (refs.includes(removedId)) {
@@ -11528,9 +11603,9 @@ async function configCommand() {
     contentMetadataChanged = previousContent.preset !== newSelection.preset || previousContent.projectType !== newSelection.projectType || previousContent.teamSize !== newSelection.teamSize;
     if (contentChanges.added.length > 0 || contentChanges.removed.length > 0) {
       const canonicalAgentsMd = await generateCanonicalAgentsMd(agentsDir);
-      await safeWriteFile(join25(agentsDir, "AGENTS.md"), canonicalAgentsMd);
+      await safeWriteFile(join27(agentsDir, "AGENTS.md"), canonicalAgentsMd);
       const rootAgentsMd = await generateRootAgentsMd(agentsDir);
-      await safeWriteFile(join25(rootDir, "AGENTS.md"), rootAgentsMd.full, {
+      await safeWriteFile(join27(rootDir, "AGENTS.md"), rootAgentsMd.full, {
         managedContent: rootAgentsMd.inner
       });
     }
@@ -11598,7 +11673,7 @@ async function configCommand() {
   if (manifest.worktree?.enabled) {
     const wtContent = await generateWorktreeInclude(manifest, rootDir);
     const wtManaged = extractManagedContent(wtContent);
-    await safeWriteFile(join25(rootDir, WORKTREE_INCLUDE_FILE), wtContent, {
+    await safeWriteFile(join27(rootDir, WORKTREE_INCLUDE_FILE), wtContent, {
       managedContent: wtManaged
     });
   }
@@ -11764,7 +11839,7 @@ async function configCommand() {
         ]);
         if (editIdentity === "detect") {
           for (const repo2 of wsManifestFinal.repos) {
-            const identity = detectRepoGitIdentity(join25(rootDir, repo2.path));
+            const identity = detectRepoGitIdentity(join27(rootDir, repo2.path));
             repo2.owner = identity.owner || void 0;
             repo2.repo = identity.repo || void 0;
             repo2.defaultBranch = identity.defaultBranch || void 0;
@@ -11863,7 +11938,7 @@ async function configCommand() {
 init_hatchJson();
 init_adapters();
 import { appendFile as appendFile2, readFile as readFile23, stat as stat7, readdir as readdir12 } from "fs/promises";
-import { join as join27 } from "path";
+import { join as join29 } from "path";
 import { execFileSync as execFileSync5 } from "child_process";
 import chalk9 from "chalk";
 
@@ -11925,10 +12000,10 @@ init_integrity();
 // src/integrity/provenance.ts
 init_safeWrite();
 import { readFile as readFile22 } from "fs/promises";
-import { join as join26, relative as relative5, posix as posix2, sep as sep2 } from "path";
+import { join as join28, relative as relative6, posix as posix2, sep as sep2 } from "path";
 var PROVENANCE_FILE = ".provenance.json";
 function normalizeToRepoPath(absPath, rootDir) {
-  const rel = relative5(rootDir, absPath);
+  const rel = relative6(rootDir, absPath);
   return sep2 === "/" ? rel : rel.split(sep2).join(posix2.sep);
 }
 function buildProvenanceManifest(hatchVersion, rootDir, perAdapterOutputs) {
@@ -11956,7 +12031,7 @@ function buildProvenanceManifest(hatchVersion, rootDir, perAdapterOutputs) {
   };
 }
 async function writeProvenanceManifest(agentsDir, manifest) {
-  const filePath = join26(agentsDir, PROVENANCE_FILE);
+  const filePath = join28(agentsDir, PROVENANCE_FILE);
   await atomicWriteFile(filePath, JSON.stringify(manifest, null, 2) + "\n");
 }
 
@@ -11972,7 +12047,7 @@ init_phaseOutputSchema();
 init_retryWithBackoff();
 init_ui();
 async function checkSpecFreshness(rootDir) {
-  const specsDir = join27(rootDir, "docs", "specs");
+  const specsDir = join29(rootDir, "docs", "specs");
   try {
     await stat7(specsDir);
   } catch {
@@ -11984,7 +12059,7 @@ async function checkSpecFreshness(rootDir) {
     for (const entry of entries) {
       if (!entry.isFile() || !entry.name.endsWith(".md")) continue;
       const parentPath = entry.parentPath ?? entry.path ?? specsDir;
-      const fileStat = await stat7(join27(parentPath, entry.name));
+      const fileStat = await stat7(join29(parentPath, entry.name));
       if (fileStat.mtimeMs < oldestSpecMtime) {
         oldestSpecMtime = fileStat.mtimeMs;
       }
@@ -12008,7 +12083,7 @@ async function checkSpecFreshness(rootDir) {
 }
 async function appendFailure2(agentsDir, phase, error2, tool) {
   try {
-    const logPath = join27(agentsDir, FAILURE_LOG_FILE);
+    const logPath = join29(agentsDir, FAILURE_LOG_FILE);
     const entry = createFailureLogEntry(phase, error2, {
       tool,
       version: HATCH3R_VERSION
@@ -12048,7 +12123,7 @@ async function syncCommand(opts = {}) {
       `This repository appears to be managed by a workspace at ${wsContext.workspaceRoot ?? ".."}. Run ${chalk9.cyan("hatch3r sync")} from the workspace root to sync all repos.`
     );
   }
-  const agentsDir = join27(rootDir, AGENTS_DIR);
+  const agentsDir = join29(rootDir, AGENTS_DIR);
   const manifest = await readManifest(rootDir);
   if (!manifest) {
     error("No .agents/hatch.json found.");
@@ -12092,8 +12167,8 @@ async function syncCommand(opts = {}) {
   const diffBefore = /* @__PURE__ */ new Map();
   const diffAfter = /* @__PURE__ */ new Map();
   if (opts.diff) {
-    diffBefore.set("AGENTS.md", await readFileOrNull2(join27(rootDir, "AGENTS.md")));
-    diffBefore.set(`${AGENTS_DIR}/AGENTS.md`, await readFileOrNull2(join27(agentsDir, "AGENTS.md")));
+    diffBefore.set("AGENTS.md", await readFileOrNull2(join29(rootDir, "AGENTS.md")));
+    diffBefore.set(`${AGENTS_DIR}/AGENTS.md`, await readFileOrNull2(join29(agentsDir, "AGENTS.md")));
   }
   const s1 = createSpinner(step(++currentStep, totalSteps, "Syncing AGENTS.md..."));
   s1.start();
@@ -12107,18 +12182,18 @@ async function syncCommand(opts = {}) {
       diffAfter.set(`${AGENTS_DIR}/AGENTS.md`, canonicalAgentsMd);
     }
   } else {
-    const agentsMdResult = await safeWriteFile(join27(rootDir, "AGENTS.md"), rootAgentsMd.full, {
+    const agentsMdResult = await safeWriteFile(join29(rootDir, "AGENTS.md"), rootAgentsMd.full, {
       managedContent: rootAgentsMd.inner
     });
     if (agentsMdResult.warning) warn(agentsMdResult.warning);
     results.push({ path: "AGENTS.md", action: agentsMdResult.action });
     const canonicalAgentsMd = await generateCanonicalAgentsMd(agentsDir);
-    const canonicalResult = await safeWriteFile(join27(agentsDir, "AGENTS.md"), canonicalAgentsMd);
+    const canonicalResult = await safeWriteFile(join29(agentsDir, "AGENTS.md"), canonicalAgentsMd);
     if (canonicalResult.warning) warn(canonicalResult.warning);
     results.push({ path: `${AGENTS_DIR}/AGENTS.md`, action: canonicalResult.action });
     if (opts.diff) {
-      diffAfter.set("AGENTS.md", await readFileOrNull2(join27(rootDir, "AGENTS.md")));
-      diffAfter.set(`${AGENTS_DIR}/AGENTS.md`, await readFileOrNull2(join27(agentsDir, "AGENTS.md")));
+      diffAfter.set("AGENTS.md", await readFileOrNull2(join29(rootDir, "AGENTS.md")));
+      diffAfter.set(`${AGENTS_DIR}/AGENTS.md`, await readFileOrNull2(join29(agentsDir, "AGENTS.md")));
     }
   }
   s1.succeed(step(currentStep, totalSteps, opts.dryRun ? "AGENTS.md (dry run)" : "AGENTS.md synced"));
@@ -12199,16 +12274,16 @@ async function syncCommand(opts = {}) {
           for (const out of outputs) {
             results.push({ path: out.path, action: "dry-run" });
             if (opts.diff) {
-              diffBefore.set(out.path, await readFileOrNull2(join27(rootDir, out.path)));
+              diffBefore.set(out.path, await readFileOrNull2(join29(rootDir, out.path)));
               diffAfter.set(out.path, out.content);
             }
           }
         } else {
           for (const out of outputs) {
             if (opts.diff) {
-              diffBefore.set(out.path, await readFileOrNull2(join27(rootDir, out.path)));
+              diffBefore.set(out.path, await readFileOrNull2(join29(rootDir, out.path)));
             }
-            const fullPath = join27(rootDir, out.path);
+            const fullPath = join29(rootDir, out.path);
             if (out.managedContent) {
               const result = await safeWriteFile(fullPath, out.content, {
                 managedContent: out.managedContent
@@ -12223,7 +12298,7 @@ async function syncCommand(opts = {}) {
               results.push({ path: out.path, action: result.action });
             }
             if (opts.diff) {
-              diffAfter.set(out.path, await readFileOrNull2(join27(rootDir, out.path)));
+              diffAfter.set(out.path, await readFileOrNull2(join29(rootDir, out.path)));
             }
           }
         }
@@ -12285,7 +12360,7 @@ async function syncCommand(opts = {}) {
       const wtContent = await generateWorktreeInclude(m, rootDir);
       const wtManaged = extractManagedContent(wtContent);
       const wtResult = await safeWriteFile(
-        join27(rootDir, WORKTREE_INCLUDE_FILE),
+        join29(rootDir, WORKTREE_INCLUDE_FILE),
         wtContent,
         { managedContent: wtManaged }
       );
@@ -12346,7 +12421,7 @@ async function syncCommand(opts = {}) {
       const CUSTOMIZE_DIRS = ["agents", "commands", "skills", "rules"];
       for (const dir of CUSTOMIZE_DIRS) {
         try {
-          const files = await readdir12(join27(rootDir, ".hatch3r", dir));
+          const files = await readdir12(join29(rootDir, ".hatch3r", dir));
           for (const f of files.filter((f2) => f2.endsWith(".customize.yaml") || f2.endsWith(".customize.md"))) {
             const itemId = f.replace(/\.customize\.(yaml|md)$/, "");
             const prefixed = `hatch3r-${itemId}`;
@@ -12460,7 +12535,7 @@ init_content();
 init_paths();
 import { readdir as readdir15, readFile as readFile26, access as access11 } from "fs/promises";
 import { existsSync as existsSync3 } from "fs";
-import { dirname as dirname15, join as join30, posix as posix3 } from "path";
+import { dirname as dirname15, join as join32, posix as posix3 } from "path";
 import { fileURLToPath as fileURLToPath6 } from "url";
 import chalk10 from "chalk";
 import { parse as parseYaml4 } from "yaml";
@@ -12468,7 +12543,7 @@ import { parse as parseYaml4 } from "yaml";
 // src/content/learningsValidation.ts
 init_customization();
 import { readFile as readFile24, readdir as readdir13 } from "fs/promises";
-import { join as join28 } from "path";
+import { join as join30 } from "path";
 var MAX_LEARNING_FILE_BYTES = 65536;
 var MAX_LEARNINGS_TOTAL_BYTES = 524288;
 var MAX_LEARNING_FILE_COUNT = 50;
@@ -12572,7 +12647,7 @@ async function validateLearningsDirectory(learningsDir) {
     const nameErrors = validateLearningFileName(file);
     errors.push(...nameErrors);
     try {
-      const content = await readFile24(join28(learningsDir, file), "utf-8");
+      const content = await readFile24(join30(learningsDir, file), "utf-8");
       const byteLength = Buffer.byteLength(content, "utf-8");
       totalBytes += byteLength;
       const result = validateLearningContent(content, file);
@@ -12743,7 +12818,7 @@ function detectSecrets(envVars) {
 // src/pipeline/complianceVerification.ts
 init_agentToolAllowlist();
 import { readFile as readFile25, readdir as readdir14 } from "fs/promises";
-import { dirname as dirname14, join as join29 } from "path";
+import { dirname as dirname14, join as join31 } from "path";
 import { fileURLToPath as fileURLToPath5 } from "url";
 
 // src/pipeline/reviewLoop.ts
@@ -12782,9 +12857,9 @@ var RESILIENCE_MODULES = [
 var __dirname5 = dirname14(fileURLToPath5(import.meta.url));
 async function resolveCommandsDir() {
   const candidates = [
-    join29(__dirname5, "..", "cli", "commands"),
-    join29(__dirname5, "..", "..", "src", "cli", "commands"),
-    join29(__dirname5, "..", "cli")
+    join31(__dirname5, "..", "cli", "commands"),
+    join31(__dirname5, "..", "..", "src", "cli", "commands"),
+    join31(__dirname5, "..", "cli")
   ];
   for (const candidate of candidates) {
     try {
@@ -12805,7 +12880,7 @@ async function detectResilienceInvocations() {
   } catch {
     return invoked;
   }
-  const files = entries.filter((e) => typeof e === "string" && (e.endsWith(".ts") || e.endsWith(".js"))).map((e) => join29(commandsDir, e));
+  const files = entries.filter((e) => typeof e === "string" && (e.endsWith(".ts") || e.endsWith(".js"))).map((e) => join31(commandsDir, e));
   const patterns = {};
   for (const mod of RESILIENCE_MODULES) {
     patterns[mod] = new RegExp(`pipeline/${mod}(?:\\.js)?["']`);
@@ -12998,7 +13073,7 @@ async function validateManifest2(rootDir, manifest, result) {
   if (!manifest.tools || manifest.tools.length === 0) result.warnings.push("hatch.json: no tools configured");
   for (const managedFile of manifest.managedFiles ?? []) {
     try {
-      await access11(join30(rootDir, managedFile));
+      await access11(join32(rootDir, managedFile));
     } catch (err) {
       if (err.code !== "ENOENT") throw err;
       result.warnings.push(`Managed file missing from disk: ${managedFile}`);
@@ -13010,7 +13085,7 @@ async function validateDirectories(agentsDir, result) {
   const optionalDirs = ["commands", "prompts", "mcp", "policy", "github-agents"];
   for (const dir of requiredDirs) {
     try {
-      await access11(join30(agentsDir, dir));
+      await access11(join32(agentsDir, dir));
     } catch (err) {
       if (err.code !== "ENOENT") throw err;
       result.errors.push(`Required directory missing: .agents/${dir}/`);
@@ -13018,7 +13093,7 @@ async function validateDirectories(agentsDir, result) {
   }
   for (const dir of optionalDirs) {
     try {
-      await access11(join30(agentsDir, dir));
+      await access11(join32(agentsDir, dir));
     } catch (err) {
       if (err.code !== "ENOENT") throw err;
       result.warnings.push(`Optional directory missing: .agents/${dir}/`);
@@ -13029,12 +13104,12 @@ async function validateFrontmatter(agentsDir, result) {
   const requiredDirs = ["agents", "skills", "rules"];
   const optionalDirs = ["commands", "prompts", "mcp", "policy", "github-agents"];
   for (const dir of [...requiredDirs, ...optionalDirs]) {
-    const dirPath = join30(agentsDir, dir);
+    const dirPath = join32(agentsDir, dir);
     try {
       const entries = await readdir15(dirPath, { withFileTypes: true });
       for (const entry of entries) {
         if (entry.isFile() && entry.name.endsWith(".md")) {
-          const filePath = join30(dirPath, entry.name);
+          const filePath = join32(dirPath, entry.name);
           const content = await readFile26(filePath, "utf-8");
           if (!content.startsWith("---")) {
             result.warnings.push(`Missing frontmatter: .agents/${dir}/${entry.name}`);
@@ -13057,7 +13132,7 @@ async function validateFrontmatter(agentsDir, result) {
             }
           }
         } else if (entry.isDirectory()) {
-          const skillPath = join30(dirPath, entry.name, "SKILL.md");
+          const skillPath = join32(dirPath, entry.name, "SKILL.md");
           try {
             await access11(skillPath);
           } catch (err) {
@@ -13071,7 +13146,7 @@ async function validateFrontmatter(agentsDir, result) {
     }
   }
   try {
-    await access11(join30(agentsDir, "AGENTS.md"));
+    await access11(join32(agentsDir, "AGENTS.md"));
   } catch (err) {
     if (err.code !== "ENOENT") throw err;
     result.warnings.push("Missing .agents/AGENTS.md");
@@ -13138,7 +13213,7 @@ async function validateManagedFilePrefixes(manifest, result) {
 }
 async function validateHooks(agentsDir, manifest, result) {
   if (!manifest.features.hooks) return;
-  const hooksDir = join30(agentsDir, "hooks");
+  const hooksDir = join32(agentsDir, "hooks");
   try {
     const hookFiles = await readdir15(hooksDir);
     const mdHooks = hookFiles.filter((f) => f.endsWith(".md"));
@@ -13147,13 +13222,13 @@ async function validateHooks(agentsDir, manifest, result) {
     }
     let agentFiles;
     try {
-      const agentEntries = await readdir15(join30(agentsDir, "agents"));
+      const agentEntries = await readdir15(join32(agentsDir, "agents"));
       agentFiles = new Set(agentEntries.filter((f) => f.endsWith(".md")));
     } catch (err) {
       if (err.code !== "ENOENT") throw err;
     }
     for (const hookFile of mdHooks) {
-      const hookContent = await readFile26(join30(hooksDir, hookFile), "utf-8");
+      const hookContent = await readFile26(join32(hooksDir, hookFile), "utf-8");
       if (!hookContent.startsWith("---")) {
         result.warnings.push(`Hook missing frontmatter: .agents/hooks/${hookFile}`);
         continue;
@@ -13185,7 +13260,7 @@ async function validateHooks(agentsDir, manifest, result) {
 }
 async function validateMcp(agentsDir, manifest, result) {
   if (!manifest.features.mcp || manifest.mcp.servers.length === 0) return;
-  const mcpPath = join30(agentsDir, "mcp", "mcp.json");
+  const mcpPath = join32(agentsDir, "mcp", "mcp.json");
   try {
     const mcpContent = await readFile26(mcpPath, "utf-8");
     const mcpParsed = JSON.parse(mcpContent);
@@ -13242,7 +13317,7 @@ async function validateCustomizeYaml(rootDir, result) {
     enabled: "boolean"
   };
   for (const { dir } of CUSTOMIZATION_TYPES) {
-    const customDir = join30(rootDir, ".hatch3r", dir);
+    const customDir = join32(rootDir, ".hatch3r", dir);
     let files;
     try {
       files = await readdir15(customDir);
@@ -13252,7 +13327,7 @@ async function validateCustomizeYaml(rootDir, result) {
     }
     const yamlFiles = files.filter((f) => f.endsWith(".customize.yaml"));
     for (const file of yamlFiles) {
-      const filePath = join30(customDir, file);
+      const filePath = join32(customDir, file);
       const itemId = file.replace(".customize.yaml", "");
       let raw;
       try {
@@ -13319,13 +13394,13 @@ async function validateCustomizeYaml(rootDir, result) {
 }
 async function validateCustomizations(rootDir, agentsDir, manifest, result) {
   for (const { dir, canonical } of CUSTOMIZATION_TYPES) {
-    const customDir = join30(rootDir, ".hatch3r", dir);
+    const customDir = join32(rootDir, ".hatch3r", dir);
     try {
       const customFiles = await readdir15(customDir);
       for (const file of customFiles) {
         if (file.endsWith(".customize.yaml")) {
           const itemId = file.replace(".customize.yaml", "");
-          const canonicalPath = canonical === "skills" ? join30(agentsDir, canonical, itemId) : join30(agentsDir, canonical, `${itemId}.md`);
+          const canonicalPath = canonical === "skills" ? join32(agentsDir, canonical, itemId) : join32(agentsDir, canonical, `${itemId}.md`);
           try {
             await access11(canonicalPath);
           } catch (err) {
@@ -13353,7 +13428,7 @@ async function validateContentConsistency(rootDir, agentsDir, manifest, result)
     for (const [key, cfg] of Object.entries(contentDirs)) {
       const ids = manifest.content.items[key];
       for (const id of ids) {
-        const checkPath = cfg.strategy === "subdir" ? join30(agentsDir, cfg.dir, id, "SKILL.md") : join30(agentsDir, cfg.dir, `${id}.md`);
+        const checkPath = cfg.strategy === "subdir" ? join32(agentsDir, cfg.dir, id, "SKILL.md") : join32(agentsDir, cfg.dir, `${id}.md`);
         try {
           await access11(checkPath);
         } catch {
@@ -13366,7 +13441,7 @@ async function validateContentConsistency(rootDir, agentsDir, manifest, result)
       for (const id of ids) allContentIds.add(id);
     }
     for (const { dir } of CUSTOMIZATION_TYPES) {
-      const customDir = join30(rootDir, ".hatch3r", dir);
+      const customDir = join32(rootDir, ".hatch3r", dir);
       try {
         const files = await readdir15(customDir);
         for (const f of files.filter((f2) => f2.endsWith(".customize.yaml") || f2.endsWith(".customize.md"))) {
@@ -13380,7 +13455,7 @@ async function validateContentConsistency(rootDir, agentsDir, manifest, result)
       }
     }
   }
-  const learningsDir = join30(agentsDir, "learnings");
+  const learningsDir = join32(agentsDir, "learnings");
   const learningsResult = await validateLearningsDirectory(learningsDir);
   for (const e of learningsResult.errors) {
     result.errors.push(e);
@@ -13500,12 +13575,12 @@ async function validateDocsCounts(rootDir) {
   let checked = 0;
   const actual = {};
   const dirs = [
-    ["adapters", join30(rootDir, "src/adapters"), (e) => e.endsWith(".ts") && !["base.ts", "index.ts", "canonical.ts", "customization.ts", "types.ts", "mcp-utils.ts", "toml-utils.ts", "contextBudget.ts", "agentsmd.ts"].includes(e)],
-    ["commands", join30(rootDir, "src/cli/commands"), (e) => e.endsWith(".ts")],
-    ["agents", join30(rootDir, "agents"), (e) => e.endsWith(".md")],
-    ["skills", join30(rootDir, "skills"), (e) => true],
-    ["rules", join30(rootDir, "rules"), (e) => e.endsWith(".md")],
-    ["hooks", join30(rootDir, "hooks"), (e) => e.endsWith(".md")]
+    ["adapters", join32(rootDir, "src/adapters"), (e) => e.endsWith(".ts") && !["base.ts", "index.ts", "canonical.ts", "customization.ts", "types.ts", "mcp-utils.ts", "toml-utils.ts", "contextBudget.ts", "agentsmd.ts"].includes(e)],
+    ["commands", join32(rootDir, "src/cli/commands"), (e) => e.endsWith(".ts")],
+    ["agents", join32(rootDir, "agents"), (e) => e.endsWith(".md")],
+    ["skills", join32(rootDir, "skills"), (e) => true],
+    ["rules", join32(rootDir, "rules"), (e) => e.endsWith(".md")],
+    ["hooks", join32(rootDir, "hooks"), (e) => e.endsWith(".md")]
   ];
   for (const [name, dir, filter] of dirs) {
     try {
@@ -13519,7 +13594,7 @@ async function validateDocsCounts(rootDir) {
       actual[name] = 0;
     }
   }
-  const readmePath = join30(rootDir, "README.md");
+  const readmePath = join32(rootDir, "README.md");
   try {
     const readme = await readFile26(readmePath, "utf-8");
     const countPatterns = [
@@ -13593,11 +13668,11 @@ async function validateCommand(opts) {
     }
     return;
   }
-  const agentsDir = join30(rootDir, AGENTS_DIR);
+  const agentsDir = join32(rootDir, AGENTS_DIR);
   const result = { errors: [], warnings: [] };
   const spinner = jsonMode ? null : createSpinner("Validating .agents/ structure...");
   spinner?.start();
-  const cwdIsFrameworkSource = existsSync3(join30(rootDir, "agents")) && existsSync3(join30(rootDir, "skills")) && existsSync3(join30(rootDir, "rules")) && existsSync3(join30(rootDir, "commands"));
+  const cwdIsFrameworkSource = existsSync3(join32(rootDir, "agents")) && existsSync3(join32(rootDir, "skills")) && existsSync3(join32(rootDir, "rules")) && existsSync3(join32(rootDir, "commands"));
   try {
     await access11(agentsDir);
   } catch (err) {
@@ -13752,7 +13827,7 @@ async function validateCommand(opts) {
   let hasCustomizations = false;
   for (const { dir } of CUSTOMIZATION_TYPES) {
     try {
-      const files = await readdir15(join30(rootDir, ".hatch3r", dir));
+      const files = await readdir15(join32(rootDir, ".hatch3r", dir));
       if (files.some((f) => f.endsWith(".customize.yaml") || f.endsWith(".customize.md"))) {
         hasCustomizations = true;
         break;
@@ -13818,7 +13893,7 @@ async function validateCommand(opts) {
   }
 }
 async function validateEnvMcpSecrets(rootDir, result) {
-  const envMcpPath = join30(rootDir, ".env.mcp");
+  const envMcpPath = join32(rootDir, ".env.mcp");
   if (!existsSync3(envMcpPath)) return;
   try {
     const raw = await readFile26(envMcpPath, "utf-8");
@@ -13838,7 +13913,7 @@ async function validateEnvMcpSecrets(rootDir, result) {
 async function validateCanonicalDescriptionQuality(rootDir, result) {
   const __filename = fileURLToPath6(import.meta.url);
   const packageRoot = findPackageRoot(dirname15(__filename));
-  const canonicalRoot = existsSync3(join30(rootDir, "agents")) && existsSync3(join30(rootDir, "skills")) && existsSync3(join30(rootDir, "rules")) && existsSync3(join30(rootDir, "commands")) ? rootDir : packageRoot;
+  const canonicalRoot = existsSync3(join32(rootDir, "agents")) && existsSync3(join32(rootDir, "skills")) && existsSync3(join32(rootDir, "rules")) && existsSync3(join32(rootDir, "commands")) ? rootDir : packageRoot;
   try {
     const index = await buildContentIndex(canonicalRoot);
     if (index.items.length === 0) return;
@@ -13884,7 +13959,7 @@ init_pipelineTimeout();
 init_phaseOutputSchema();
 init_retryWithBackoff();
 init_ui();
-import { join as join31 } from "path";
+import { join as join33 } from "path";
 import chalk11 from "chalk";
 async function runVerifyPass(agentsDir) {
   const results = await verifyIntegrity(agentsDir);
@@ -13938,7 +14013,7 @@ async function verifyCommand(options = {}) {
     DEFAULT_PIPELINE_TIMEOUT_MS
   );
   const rootDir = process.cwd();
-  const agentsDir = join31(rootDir, AGENTS_DIR);
+  const agentsDir = join33(rootDir, AGENTS_DIR);
   const spinner = createSpinner("Verifying file integrity...");
   spinner.start();
   const manifest = await readIntegrityManifest(agentsDir);
@@ -14075,7 +14150,7 @@ init_managedBlocks();
 init_integrity();
 init_ui();
 import { access as access12, readFile as readFile27, readdir as readdir16, stat as stat8 } from "fs/promises";
-import { join as join32 } from "path";
+import { join as join34 } from "path";
 import chalk12 from "chalk";
 async function dirCharCount(dir) {
   let total = 0;
@@ -14086,7 +14161,7 @@ async function dirCharCount(dir) {
     return 0;
   }
   for (const entry of entries) {
-    const fullPath = join32(dir, entry.name);
+    const fullPath = join34(dir, entry.name);
     if (entry.isDirectory()) {
       total += await dirCharCount(fullPath);
     } else if (entry.isFile()) {
@@ -14122,7 +14197,7 @@ async function runFastStatusCheck(rootDir, agentsDir, manifest) {
     verbose(`${tool}: ${paths.length} output path(s) to check (fast path)`);
     fileLines.push(chalk12.bold(`${tool}:`));
     for (const p of paths) {
-      const destPath = join32(rootDir, p);
+      const destPath = join34(rootDir, p);
       try {
         const fileStat = await stat8(destPath);
         if (fileStat.mtimeMs > sealMs) {
@@ -14150,7 +14225,7 @@ async function runDeepStatusCheck(rootDir, agentsDir, manifest) {
     verbose(`${tool}: ${outputs.length} output file(s) to check`);
     fileLines.push(chalk12.bold(`${tool}:`));
     for (const out of outputs) {
-      const destPath = join32(rootDir, out.path);
+      const destPath = join34(rootDir, out.path);
       try {
         const existing = await readFile27(destPath, "utf-8");
         const existingBlock = extractManagedBlock(existing);
@@ -14175,7 +14250,7 @@ async function statusCommand(opts) {
   setVerbose(!!opts?.verbose);
   printBanner(true);
   const rootDir = process.cwd();
-  const agentsDir = join32(rootDir, AGENTS_DIR);
+  const agentsDir = join34(rootDir, AGENTS_DIR);
   const manifest = await readManifest(rootDir);
   if (!manifest) {
     error("No .agents/hatch.json found.");
@@ -14228,7 +14303,7 @@ async function statusCommand(opts) {
     console.log();
   }
   if (manifest.tools.includes("codex")) {
-    const overridePath = join32(rootDir, "AGENTS.override.md");
+    const overridePath = join34(rootDir, "AGENTS.override.md");
     try {
       await access12(overridePath);
       warn(
@@ -14319,7 +14394,7 @@ function createProgram() {
   program2.command("init").description("Install a complete agent setup into the current repo (first-run: creates .agents/ directory)").option(
     "--tools <tools>",
     `Comma-separated tools (${TOOL_CHOICES})`
-  ).option("--yes", "Skip interactive prompts, use defaults").option("--quick", "Skip all prompts and use smart defaults (alias for --yes)").option("--default", "Skip all prompts and use smart defaults (alias for --yes)").option("--preset <preset>", "Content preset: minimal, standard, full (default: full)").option("--project-type <type>", "Project type: greenfield, brownfield").option("--team-size <size>", "Team size: solo, team").option("--workspace", "Initialize as a multi-repo workspace").action(initCommand);
+  ).option("--yes", "Skip interactive prompts, use defaults").option("--quick", "Skip all prompts and use smart defaults (alias for --yes)").option("--default", "Skip all prompts and use smart defaults (alias for --yes)").option("--preset <preset>", "Content preset: minimal, standard, full (default: full)").option("--project-type <type>", "Project type: greenfield, brownfield").option("--team-size <size>", "Team size: solo, team").option("--worktree", "Enable git worktree file isolation (overrides tool auto-detect)").option("--no-worktree", "Disable git worktree file isolation").option("--workspace", "Initialize as a multi-repo workspace").action(initCommand);
   program2.command("sync").description("Re-generate tool outputs from canonical .agents/ state (run after editing .agents/)").option("--repos [paths...]", "Sync workspace content to sub-repos (all opted-in if no paths given)").option("--dry-run", "Show what would change without modifying files").option("--diff", "Show a before/after diff summary for each generated file").option("--force", "Overwrite locally modified files in sub-repos").option("--minimal", "Generate stripped-down output (no comments, minimal formatting) to reduce token usage").option("--strict-budget", "Fail sync if any adapter's generated output exceeds its context budget (default: warn)").option("--verbose", "Show detailed output for each file processed").action(syncCommand);
   program2.command("status").description("Check sync status between canonical .agents/ and generated files").option("--verbose", "Show detailed per-file status information").option("--deep", "Regenerate every adapter's output in-memory to compare byte-for-byte (slower; default uses integrity-manifest fast path)").action(statusCommand);
   program2.command("update").description("Pull latest hatch3r templates with safe merge (preserves customizations)").option("--yes", "Skip interactive prompts, use defaults").option("--diff", "Show a before/after diff summary for each generated file").option("--force", "Override the preflight integrity check and proceed despite drift").option("--offline, --skip-fetch", "Skip the package fetch step; regenerate only from already-installed canonical content").option("--dry-run", "Preview what would change (added/modified/unchanged per adapter) without writing files").action(updateCommand);