architectonic 0.0.3 → 0.0.5

package/README.md

@@ -12,8 +12,9 @@ skills     -- reusable procedures and capabilities
 ```
 
 The initial placeholder releases were intentionally minimal. Starting in
-`0.0.3`, `architectonic add` becomes real: it clones the selected layer
-repositories into a target directory and records them in `architectonic.json`.
+`0.0.5`, `architectonic` can initialize a workspace, add layers, inspect the
+local manifest, repair light manifest drift, update safely, and remove layers
+without trampling local forks.
 
 ## Command shape
 
@@ -25,9 +26,11 @@ architectonic add identity
 architectonic add project
 architectonic add skills
 architectonic add teleology identity skills
+architectonic init
 architectonic doctor
 architectonic list
 architectonic update
+architectonic remove
 ```
 
 `add` is explicit and leaves room for future verbs such as `doctor`, `list`,
@@ -44,9 +47,18 @@ npx architectonic add project
 npx architectonic add skills
 npx architectonic add teleology identity skills
 npx architectonic add skills --dir ./vendor
+npx architectonic add teleology --source npm
+npx architectonic init MyWorkspace
+npx architectonic init --preset company
+npx architectonic list
+npx architectonic doctor
+npx architectonic doctor --fix
+npx architectonic update
+npx architectonic update --dry-run
+npx architectonic remove skills
 ```
 
-`add` clones from the Architectonic GitHub organization into the current
+`add` installs from the Architectonic GitHub organization into the current
 directory by default:
 
 ```text
@@ -62,6 +74,56 @@ directory by default:
 If a target directory already exists, the command stops instead of silently
 overwriting it.
 
+## Sources
+
+`add` supports two source modes:
+
+```text
+--source git   # clone from GitHub or another git base
+--source npm   # pack and extract from npm packages
+```
+
+The default is `git`.
+
+Environment overrides:
+
+```text
+ARCHITECTONIC_SOURCE_BASE   # override the git source base
+ARCHITECTONIC_NPM_BASE      # override the npm package base or local package root
+ARCHITECTONIC_ADD_SOURCE    # change the default source mode
+```
+
+`list` reads `architectonic.json` and shows installed layers.
+
+`doctor` verifies that each recorded layer still exists and that the installed
+package metadata matches the expected layer. `doctor --fix` repairs light
+manifest drift such as stale package names or recoverable default paths.
+
+`init` creates a workspace root, installs a preset, and seeds a top-level
+`README.md` and `AGENTS.md`.
+
+Supported presets:
+
+```text
+solo     # teleology + identity + project + skills
+company  # teleology + project + skills
+project  # project + skills
+agent    # identity + skills
+```
+
+`update` is conservative by design:
+
+```text
+git layers: only fast-forward clean git worktrees
+npm layers: report newer packages but do not overwrite local forks
+```
+
+If a user has modified an installed instance, `update` should skip it rather
+than flatten their divergence.
+
+`remove` deletes a recorded layer and updates the manifest. If the layer is a
+dirty git worktree, it refuses unless `--force` is explicit.
+
 ## Run vs install
 
 ```text

package/bin/architectonic.js

@@ -4,12 +4,19 @@ import fs from "node:fs";
 import path from "node:path";
 import { spawnSync } from "node:child_process";
 
-const VERSION = "0.0.3";
+const VERSION = "0.0.5";
 const args = process.argv.slice(2);
 const [command, ...rest] = args;
 const supported = ["teleology", "identity", "project", "skills"];
 const supportedSet = new Set(supported);
 const repoBase = process.env.ARCHITECTONIC_SOURCE_BASE || "https://github.com/architectonic";
+const npmBase = process.env.ARCHITECTONIC_NPM_BASE || "";
+const packageMap = {
+  teleology: "teleology",
+  identity: "architectonic-identity",
+  project: "architectonic-project",
+  skills: "architectonic-skills",
+};
 
 function printHelp() {
   console.log(`architectonic ${VERSION}
@@ -22,6 +29,13 @@ Usage:
   npx architectonic add <teleology|identity|project|skills>
   npx architectonic add teleology identity skills
   npx architectonic add skills --dir ./vendor
+  npx architectonic add teleology --source npm
+  npx architectonic init [name]
+  npx architectonic list
+  npx architectonic doctor
+  npx architectonic doctor --fix
+  npx architectonic update
+  npx architectonic remove <layer>
 
 Layers:
   teleology  purpose, principles, doctrine, governance
@@ -35,13 +49,18 @@ Run vs install:
   npm install -g architectonic install globally
 
 What add does:
-  Clones the selected layer repositories into the target directory
-  and records them in architectonic.json.`);
+  Installs the selected layer repositories into the target directory
+  from git or npm sources and records them in architectonic.json.`);
+}
+
+function printUsageError(message) {
+  throw new Error(`${message}\nRun \`architectonic help\` for usage.`);
 }
 
 function parseAddArgs(tokens) {
   const targets = [];
   let installDir = process.cwd();
+  let source = process.env.ARCHITECTONIC_ADD_SOURCE || "git";
 
   for (let index = 0; index < tokens.length; index += 1) {
     const token = tokens[index];
@@ -62,13 +81,173 @@ function parseAddArgs(tokens) {
       installDir = path.resolve(token.slice("--out=".length));
       continue;
     }
+    if (token === "--source") {
+      const next = tokens[index + 1];
+      if (!next) {
+        throw new Error("Missing value for --source");
+      }
+      source = next;
+      index += 1;
+      continue;
+    }
+    if (token.startsWith("--source=")) {
+      source = token.slice("--source=".length);
+      continue;
+    }
     if (token.startsWith("-")) {
       throw new Error(`Unknown option: ${token}`);
     }
     targets.push(token);
   }
 
-  return { targets, installDir };
+  return { targets, installDir, source };
+}
+
+function parseInitArgs(tokens) {
+  let installDir = process.cwd();
+  let source = process.env.ARCHITECTONIC_ADD_SOURCE || "git";
+  let preset = "solo";
+  let workspaceName = "";
+
+  for (let index = 0; index < tokens.length; index += 1) {
+    const token = tokens[index];
+    if (token === "--dir" || token === "--out") {
+      const next = tokens[index + 1];
+      if (!next) {
+        throw new Error(`Missing value for ${token}`);
+      }
+      installDir = path.resolve(next);
+      index += 1;
+      continue;
+    }
+    if (token.startsWith("--dir=")) {
+      installDir = path.resolve(token.slice("--dir=".length));
+      continue;
+    }
+    if (token.startsWith("--out=")) {
+      installDir = path.resolve(token.slice("--out=".length));
+      continue;
+    }
+    if (token === "--source") {
+      const next = tokens[index + 1];
+      if (!next) {
+        throw new Error("Missing value for --source");
+      }
+      source = next;
+      index += 1;
+      continue;
+    }
+    if (token.startsWith("--source=")) {
+      source = token.slice("--source=".length);
+      continue;
+    }
+    if (token === "--preset") {
+      const next = tokens[index + 1];
+      if (!next) {
+        throw new Error("Missing value for --preset");
+      }
+      preset = next;
+      index += 1;
+      continue;
+    }
+    if (token.startsWith("--preset=")) {
+      preset = token.slice("--preset=".length);
+      continue;
+    }
+    if (token.startsWith("-")) {
+      throw new Error(`Unknown option: ${token}`);
+    }
+    if (!workspaceName) {
+      workspaceName = token;
+      continue;
+    }
+    throw new Error(`Unexpected argument: ${token}`);
+  }
+
+  if (workspaceName) {
+    installDir = path.resolve(installDir, workspaceName);
+  }
+
+  return { installDir, source, preset, workspaceName };
+}
+
+function parseDoctorArgs(tokens) {
+  let installDir = process.cwd();
+  let fix = false;
+
+  for (let index = 0; index < tokens.length; index += 1) {
+    const token = tokens[index];
+    if (token === "--fix") {
+      fix = true;
+      continue;
+    }
+    if (token.startsWith("-")) {
+      throw new Error(`Unknown option: ${token}`);
+    }
+    installDir = path.resolve(token);
+  }
+
+  return { installDir, fix };
+}
+
+function parseUpdateArgs(tokens) {
+  let installDir = process.cwd();
+  let dryRun = false;
+
+  for (let index = 0; index < tokens.length; index += 1) {
+    const token = tokens[index];
+    if (token === "--dry-run") {
+      dryRun = true;
+      continue;
+    }
+    if (token.startsWith("-")) {
+      throw new Error(`Unknown option: ${token}`);
+    }
+    installDir = path.resolve(token);
+  }
+
+  return { installDir, dryRun };
+}
+
+function parseRemoveArgs(tokens) {
+  let installDir = process.cwd();
+  let force = false;
+  let target = "";
+
+  for (let index = 0; index < tokens.length; index += 1) {
+    const token = tokens[index];
+    if (token === "--force") {
+      force = true;
+      continue;
+    }
+    if (token === "--dir" || token === "--out") {
+      const next = tokens[index + 1];
+      if (!next) {
+        throw new Error(`Missing value for ${token}`);
+      }
+      installDir = path.resolve(next);
+      index += 1;
+      continue;
+    }
+    if (token.startsWith("--dir=")) {
+      installDir = path.resolve(token.slice("--dir=".length));
+      continue;
+    }
+    if (token.startsWith("--out=")) {
+      installDir = path.resolve(token.slice("--out=".length));
+      continue;
+    }
+    if (token.startsWith("-")) {
+      throw new Error(`Unknown option: ${token}`);
+    }
+    if (!target) {
+      target = token;
+      continue;
+    }
+    throw new Error(`Unexpected argument: ${token}`);
+  }
+
+  return { installDir, force, target };
 }
 
 function ensureGitAvailable() {
@@ -78,6 +257,20 @@ function ensureGitAvailable() {
   }
 }
 
+function ensureNpmAvailable() {
+  const result = spawnSync("npm", ["--version"], { encoding: "utf8", shell: true });
+  if (result.status !== 0) {
+    throw new Error("npm is required on PATH for `architectonic add --source npm`.");
+  }
+}
+
+function ensureTarAvailable() {
+  const result = spawnSync("tar", ["--version"], { encoding: "utf8" });
+  if (result.status !== 0) {
+    throw new Error("tar is required on PATH for npm package extraction.");
+  }
+}
+
 function repoUrlFor(target) {
   const normalizedBase = repoBase.replace(/\\/g, "/");
   if (/^(?:[A-Za-z]:\/|\/|\.{1,2}\/)/.test(normalizedBase)) {
@@ -86,10 +279,31 @@ function repoUrlFor(target) {
   return `${normalizedBase}/${target}.git`;
 }
 
+function packageSpecFor(target) {
+  const packageName = packageMap[target];
+  if (!packageName) {
+    throw new Error(`No npm package mapping defined for ${target}`);
+  }
+  if (!npmBase) {
+    return packageName;
+  }
+  const normalizedBase = npmBase.replace(/\\/g, "/");
+  if (/^(?:[A-Za-z]:\/|\/|\.{1,2}\/)/.test(normalizedBase)) {
+    return path.resolve(normalizedBase, target);
+  }
+  return normalizedBase.endsWith("/")
+    ? `${normalizedBase}${packageName}`
+    : `${normalizedBase}/${packageName}`;
+}
+
 function targetPathFor(installDir, target) {
   return path.join(installDir, target);
 }
 
+function manifestPathFor(installDir) {
+  return path.join(installDir, "architectonic.json");
+}
+
 function readManifest(manifestPath) {
   if (!fs.existsSync(manifestPath)) {
     return {
@@ -106,6 +320,14 @@ function writeManifest(manifestPath, manifest) {
   fs.writeFileSync(manifestPath, `${JSON.stringify(manifest, null, 2)}\n`, "utf8");
 }
 
+function readJson(filePath) {
+  return JSON.parse(fs.readFileSync(filePath, "utf8"));
+}
+
+function pathExists(filePath) {
+  return fs.existsSync(filePath);
+}
+
 function cloneLayer(target, installDir) {
   const repoUrl = repoUrlFor(target);
   const targetPath = targetPathFor(installDir, target);
@@ -129,41 +351,171 @@ function cloneLayer(target, installDir) {
     name: target,
     repo: repoUrl,
     path: targetPath,
+    source: "git",
   };
 }
 
-function addCommand(tokens) {
-  const { targets, installDir } = parseAddArgs(tokens);
+function packNpmLayer(target, installDir) {
+  const packageSpec = packageSpecFor(target);
+  const targetPath = targetPathFor(installDir, target);
+  const tempRoot = fs.mkdtempSync(path.join(installDir, "architectonic-npm-"));
+  const pack = spawnSync("npm", ["pack", packageSpec, "--pack-destination", tempRoot], {
+    cwd: installDir,
+    encoding: "utf8",
+    stdio: "pipe",
+    shell: true,
+  });
 
-  if (!targets.length) {
-    throw new Error("Specify one or more layers: teleology, identity, project, skills");
+  if (pack.status !== 0) {
+    const detail = (pack.stderr || pack.stdout || "").trim();
+    throw new Error(`Failed to pack ${packageSpec}${detail ? `\n${detail}` : ""}`);
   }
 
-  const invalid = targets.filter((target) => !supportedSet.has(target));
-  if (invalid.length) {
-    throw new Error(`Unknown layer(s): ${invalid.join(", ")}\nSupported layers: ${supported.join(", ")}`);
+  const tgzName = (pack.stdout || "").trim().split(/\r?\n/).filter(Boolean).pop();
+  if (!tgzName) {
+    throw new Error(`npm pack did not return a tarball name for ${packageSpec}`);
   }
 
-  ensureGitAvailable();
+  const tgzPath = path.join(tempRoot, tgzName);
+  if (!fs.existsSync(tgzPath)) {
+    throw new Error(`Packed tarball not found: ${tgzPath}`);
+  }
+
+  if (fs.existsSync(targetPath)) {
+    throw new Error(`Target already exists: ${targetPath}`);
+  }
+
+  fs.mkdirSync(targetPath, { recursive: true });
+  const extract = spawnSync("tar", ["-xzf", tgzPath, "-C", targetPath], {
+    cwd: installDir,
+    encoding: "utf8",
+    stdio: "pipe",
+  });
+
+  if (extract.status !== 0) {
+    const detail = (extract.stderr || extract.stdout || "").trim();
+    throw new Error(`Failed to extract ${tgzPath}${detail ? `\n${detail}` : ""}`);
+  }
+
+  const extractedPackageDir = path.join(targetPath, "package");
+  if (!fs.existsSync(extractedPackageDir)) {
+    throw new Error(`Expected extracted package directory at ${extractedPackageDir}`);
+  }
+
+  for (const entry of fs.readdirSync(extractedPackageDir, { withFileTypes: true })) {
+    const from = path.join(extractedPackageDir, entry.name);
+    const to = path.join(targetPath, entry.name);
+    fs.renameSync(from, to);
+  }
+  fs.rmdirSync(extractedPackageDir);
+  fs.rmSync(tempRoot, { recursive: true, force: true });
+
+  return {
+    name: target,
+    repo: packageSpec,
+    path: targetPath,
+    source: "npm",
+  };
+}
+
+function readInstalledPackageName(layerPath) {
+  const packageJsonPath = path.join(layerPath, "package.json");
+  if (!fs.existsSync(packageJsonPath)) {
+    return null;
+  }
+  try {
+    return readJson(packageJsonPath).name || null;
+  } catch {
+    return null;
+  }
+}
+
+function readInstalledVersion(layerPath) {
+  const packageJsonPath = path.join(layerPath, "package.json");
+  if (!fs.existsSync(packageJsonPath)) {
+    return null;
+  }
+  try {
+    return readJson(packageJsonPath).version || null;
+  } catch {
+    return null;
+  }
+}
+
+function hasGitRepo(layerPath) {
+  return pathExists(path.join(layerPath, ".git"));
+}
+
+function gitResult(args, cwd) {
+  return spawnSync("git", args, {
+    cwd,
+    encoding: "utf8",
+    stdio: "pipe",
+  });
+}
+
+function isGitWorktreeDirty(layerPath) {
+  const result = gitResult(["status", "--porcelain"], layerPath);
+  if (result.status !== 0) {
+    return null;
+  }
+  return Boolean((result.stdout || "").trim());
+}
+
+function packageMetaFor(target, layerPath) {
+  return {
+    expectedPackageName: packageMap[target] || null,
+    packageName: readInstalledPackageName(layerPath),
+    version: readInstalledVersion(layerPath),
+  };
+}
+
+function relativeManifestPath(installDir, absolutePath) {
+  return `./${path.relative(installDir, absolutePath).replace(/\\/g, "/")}`;
+}
+
+function ensureInstallPrereqs(source) {
+  if (source === "git") {
+    ensureGitAvailable();
+    return;
+  }
+  if (source === "npm") {
+    ensureNpmAvailable();
+    ensureTarAvailable();
+    return;
+  }
+  throw new Error(`Unsupported source: ${source}. Use git or npm.`);
+}
+
+function updateManifestLayerRecord(manifest, installDir, layerName, absoluteLayerPath, source, refOverride = null) {
+  manifest.layers[layerName] = {
+    source,
+    ref: refOverride ?? manifest.layers[layerName]?.ref ?? (source === "git" ? repoUrlFor(layerName) : packageSpecFor(layerName)),
+    path: relativeManifestPath(installDir, absoluteLayerPath),
+    installed_at: new Date().toISOString(),
+    package_name: readInstalledPackageName(absoluteLayerPath),
+  };
+}
+
+function installTargets(targets, installDir, source) {
+  ensureInstallPrereqs(source);
   fs.mkdirSync(installDir, { recursive: true });
 
   const installed = [];
   for (const target of targets) {
-    console.log(`Adding ${target}...`);
-    installed.push(cloneLayer(target, installDir));
+    console.log(`Adding ${target} from ${source}...`);
+    installed.push(installLayer(target, installDir, source));
   }
 
-  const manifestPath = path.join(installDir, "architectonic.json");
+  const manifestPath = manifestPathFor(installDir);
   const manifest = readManifest(manifestPath);
   manifest.installed_at = new Date().toISOString();
-  manifest.source_base = repoBase;
+  manifest.last_source = source;
+  manifest.git_source_base = repoBase;
+  manifest.npm_source_base = npmBase || "registry";
 
   for (const item of installed) {
-    manifest.layers[item.name] = {
-      repo: item.repo,
-      path: `./${path.relative(installDir, item.path).replace(/\\/g, "/")}`,
-      installed_at: manifest.installed_at,
-    };
+    updateManifestLayerRecord(manifest, installDir, item.name, item.path, item.source, item.repo);
   }
 
   writeManifest(manifestPath, manifest);
@@ -173,18 +525,355 @@ function addCommand(tokens) {
   console.log(`Wrote ${manifestPath}`);
 }
 
+function installLayer(target, installDir, source) {
+  if (source === "git") {
+    return cloneLayer(target, installDir);
+  }
+  if (source === "npm") {
+    return packNpmLayer(target, installDir);
+  }
+  throw new Error(`Unsupported source: ${source}. Use git or npm.`);
+}
+
+function loadManifestFromDir(installDir) {
+  const manifestPath = manifestPathFor(installDir);
+  if (!fs.existsSync(manifestPath)) {
+    throw new Error(`No architectonic.json found in ${installDir}`);
+  }
+  return { manifestPath, manifest: readManifest(manifestPath) };
+}
+
+function addCommand(tokens) {
+  const { targets, installDir, source } = parseAddArgs(tokens);
+
+  if (!targets.length) {
+    throw new Error("Specify one or more layers: teleology, identity, project, skills");
+  }
+
+  const invalid = targets.filter((target) => !supportedSet.has(target));
+  if (invalid.length) {
+    throw new Error(`Unknown layer(s): ${invalid.join(", ")}\nSupported layers: ${supported.join(", ")}`);
+  }
+
+  installTargets(targets, installDir, source);
+}
+
+function resolvePreset(preset) {
+  const presets = {
+    solo: ["teleology", "identity", "project", "skills"],
+    company: ["teleology", "project", "skills"],
+    project: ["project", "skills"],
+    agent: ["identity", "skills"],
+  };
+  const layers = presets[preset];
+  if (!layers) {
+    throw new Error(`Unknown preset: ${preset}. Supported presets: ${Object.keys(presets).join(", ")}`);
+  }
+  return layers;
+}
+
+function writeInitFiles(installDir, workspaceName, layers) {
+  const displayName = workspaceName || path.basename(installDir);
+  const readmePath = path.join(installDir, "README.md");
+  const agentsPath = path.join(installDir, "AGENTS.md");
+
+  if (!pathExists(readmePath)) {
+    fs.writeFileSync(
+      readmePath,
+      `# ${displayName}\n\nThis workspace was initialized by \`architectonic\`.\n\nInstalled layers:\n\n${layers.map((layer) => `- ${layer}`).join("\n")}\n`,
+      "utf8",
+    );
+  }
+
+  if (!pathExists(agentsPath)) {
+    fs.writeFileSync(
+      agentsPath,
+      `# Agent Instructions\n\nRead installed layers before making structural changes.\n\nPriority order:\n1. teleology\n2. identity\n3. project\n4. skills\n`,
+      "utf8",
+    );
+  }
+}
+
+function initCommand(tokens) {
+  const { installDir, source, preset, workspaceName } = parseInitArgs(tokens);
+  if (pathExists(installDir) && fs.readdirSync(installDir).length > 0) {
+    throw new Error(`Refusing to initialize into a non-empty directory: ${installDir}`);
+  }
+  fs.mkdirSync(installDir, { recursive: true });
+  const layers = resolvePreset(preset);
+  writeInitFiles(installDir, workspaceName, layers);
+  installTargets(layers, installDir, source);
+}
+
+function listCommand(tokens) {
+  const installDir = tokens[0] ? path.resolve(tokens[0]) : process.cwd();
+  const { manifest } = loadManifestFromDir(installDir);
+  const entries = Object.entries(manifest.layers || {});
+
+  if (!entries.length) {
+    console.log("No layers installed.");
+    return;
+  }
+
+  for (const [name, layer] of entries) {
+    console.log(`${name}`);
+    console.log(`  source: ${layer.source || "unknown"}`);
+    console.log(`  path:   ${layer.path || "unknown"}`);
+    console.log(`  ref:    ${layer.ref || "unknown"}`);
+    if (layer.package_name) {
+      console.log(`  pkg:    ${layer.package_name}`);
+    }
+  }
+}
+
+function inferLayerPath(installDir, layerName) {
+  const candidate = targetPathFor(installDir, layerName);
+  return pathExists(candidate) ? candidate : null;
+}
+
+function doctorCommand(tokens) {
+  const { installDir, fix } = parseDoctorArgs(tokens);
+  const { manifestPath, manifest } = loadManifestFromDir(installDir);
+  const entries = Object.entries(manifest.layers || {});
+  let failures = 0;
+  let changed = false;
+
+  console.log(`architectonic doctor`);
+  console.log(`  root: ${installDir}`);
+  console.log(`  manifest: ${manifestPath}`);
+
+  if (!entries.length) {
+    console.log(`  [fail] no installed layers recorded`);
+    process.exit(1);
+  }
+
+  for (const [name, layer] of entries) {
+    const relativePath = String(layer.path || "");
+    const layerPath = path.resolve(installDir, relativePath);
+    const packageJsonPath = path.join(layerPath, "package.json");
+    const exists = fs.existsSync(layerPath);
+    const hasPackageJson = fs.existsSync(packageJsonPath);
+    const packageName = hasPackageJson ? readInstalledPackageName(layerPath) : null;
+    const expectedPackageName = packageMap[name];
+
+    if (!exists) {
+      const inferredPath = inferLayerPath(installDir, name);
+      if (fix && inferredPath) {
+        updateManifestLayerRecord(manifest, installDir, name, inferredPath, layer.source || "unknown", layer.ref || null);
+        changed = true;
+        console.log(`  [fix] ${name}: repointed path to ${relativeManifestPath(installDir, inferredPath)}`);
+        continue;
+      }
+      console.log(`  [fail] ${name}: missing directory ${layerPath}`);
+      failures += 1;
+      continue;
+    }
+
+    if (!hasPackageJson) {
+      console.log(`  [fail] ${name}: missing package.json`);
+      failures += 1;
+      continue;
+    }
+
+    if (packageName && expectedPackageName && packageName !== expectedPackageName) {
+      if (fix) {
+        manifest.layers[name].package_name = packageName;
+        manifest.layers[name].path = relativeManifestPath(installDir, layerPath);
+        changed = true;
+        console.log(`  [fix] ${name}: synced manifest package name to ${packageName}`);
+        continue;
+      }
+      console.log(`  [fail] ${name}: expected package ${expectedPackageName}, found ${packageName}`);
+      failures += 1;
+      continue;
+    }
+
+    if (fix) {
+      const normalizedPath = relativeManifestPath(installDir, layerPath);
+      if (manifest.layers[name].path !== normalizedPath || manifest.layers[name].package_name !== packageName) {
+        manifest.layers[name].path = normalizedPath;
+        manifest.layers[name].package_name = packageName;
+        changed = true;
+      }
+    }
+
+    console.log(`  [ok] ${name}: ${relativePath} (${layer.source || "unknown"})`);
+  }
+
+  if (fix && changed) {
+    writeManifest(manifestPath, manifest);
+    console.log(`  [write] updated manifest repairs`);
+  }
+
+  if (failures > 0) {
+    process.exit(1);
+  }
+}
+
+function updateGitLayer(layerName, layerPath, dryRun) {
+  if (!hasGitRepo(layerPath)) {
+    return { status: "skip", detail: "not a git repository" };
+  }
+  const dirty = isGitWorktreeDirty(layerPath);
+  if (dirty === null) {
+    return { status: "skip", detail: "unable to inspect git status" };
+  }
+  if (dirty) {
+    return { status: "skip", detail: "local changes detected; preserving fork" };
+  }
+  if (dryRun) {
+    return { status: "plan", detail: "would run git pull --ff-only" };
+  }
+  const result = gitResult(["pull", "--ff-only"], layerPath);
+  if (result.status !== 0) {
+    return { status: "fail", detail: (result.stderr || result.stdout || "").trim() || "git pull failed" };
+  }
+  return { status: "ok", detail: (result.stdout || "").trim() || "up to date" };
+}
+
+function getLatestNpmVersion(packageSpec) {
+  const result = spawnSync("npm", ["view", packageSpec, "version"], {
+    encoding: "utf8",
+    stdio: "pipe",
+    shell: true,
+  });
+  if (result.status !== 0) {
+    return null;
+  }
+  return (result.stdout || "").trim() || null;
+}
+
+function updateNpmLayer(layerName, layerPath) {
+  const installedVersion = readInstalledVersion(layerPath);
+  const packageSpec = packageSpecFor(layerName);
+  const latestVersion = getLatestNpmVersion(packageSpec);
+  if (!latestVersion) {
+    return { status: "skip", detail: "unable to resolve latest npm version" };
+  }
+  if (!installedVersion) {
+    return { status: "skip", detail: `latest ${latestVersion} available; local version unknown` };
+  }
+  if (installedVersion === latestVersion) {
+    return { status: "ok", detail: `already at ${installedVersion}` };
+  }
+  return {
+    status: "skip",
+    detail: `newer package ${latestVersion} available; skipped to preserve local fork (${installedVersion} installed)`,
+  };
+}
+
+function updateCommand(tokens) {
+  const { installDir, dryRun } = parseUpdateArgs(tokens);
+  const { manifestPath, manifest } = loadManifestFromDir(installDir);
+  const entries = Object.entries(manifest.layers || {});
+
+  if (!entries.length) {
+    throw new Error("No installed layers recorded.");
+  }
+
+  ensureGitAvailable();
+  ensureNpmAvailable();
+
+  let changed = false;
+  console.log(`architectonic update${dryRun ? " --dry-run" : ""}`);
+  console.log(`  root: ${installDir}`);
+
+  for (const [name, layer] of entries) {
+    const layerPath = path.resolve(installDir, String(layer.path || ""));
+    if (!pathExists(layerPath)) {
+      console.log(`  [skip] ${name}: missing directory`);
+      continue;
+    }
+
+    let outcome;
+    if (layer.source === "git") {
+      outcome = updateGitLayer(name, layerPath, dryRun);
+    } else if (layer.source === "npm") {
+      outcome = updateNpmLayer(name, layerPath);
+    } else {
+      outcome = { status: "skip", detail: `unsupported source ${layer.source || "unknown"}` };
+    }
+
+    console.log(`  [${outcome.status}] ${name}: ${outcome.detail}`);
+    if (outcome.status === "ok" && !dryRun) {
+      manifest.layers[name].installed_at = new Date().toISOString();
+      manifest.layers[name].package_name = readInstalledPackageName(layerPath);
+      changed = true;
+    }
+  }
+
+  if (changed) {
+    writeManifest(manifestPath, manifest);
+    console.log(`  [write] refreshed manifest timestamps`);
+  }
+}
+
+function removeCommand(tokens) {
+  const { installDir, force, target } = parseRemoveArgs(tokens);
+  if (!target) {
+    throw new Error("Specify a layer to remove.");
+  }
+  if (!supportedSet.has(target)) {
+    throw new Error(`Unknown layer: ${target}`);
+  }
+  const { manifestPath, manifest } = loadManifestFromDir(installDir);
+  const layer = manifest.layers[target];
+  if (!layer) {
+    throw new Error(`Layer not recorded in manifest: ${target}`);
+  }
+  const layerPath = path.resolve(installDir, String(layer.path || ""));
+  if (pathExists(layerPath) && hasGitRepo(layerPath) && !force) {
+    const dirty = isGitWorktreeDirty(layerPath);
+    if (dirty) {
+      throw new Error(`Refusing to remove ${target}: local git changes detected. Re-run with --force if you really want to delete it.`);
+    }
+  }
+  if (pathExists(layerPath)) {
+    fs.rmSync(layerPath, { recursive: true, force: true });
+  }
+  delete manifest.layers[target];
+  writeManifest(manifestPath, manifest);
+  console.log(`Removed ${target}`);
+  console.log(`Updated ${manifestPath}`);
+}
+
 try {
   if (!command || command === "help" || command === "--help" || command === "-h") {
     printHelp();
     process.exit(0);
   }
 
+  if (command === "init") {
+    initCommand(rest);
+    process.exit(0);
+  }
+
   if (command === "add") {
     addCommand(rest);
     process.exit(0);
   }
 
-  throw new Error(`Unknown command: ${command}\nRun \`architectonic help\` for usage.`);
+  if (command === "list") {
+    listCommand(rest);
+    process.exit(0);
+  }
+
+  if (command === "doctor") {
+    doctorCommand(rest);
+    process.exit(0);
+  }
+
+  if (command === "update") {
+    updateCommand(rest);
+    process.exit(0);
+  }
+
+  if (command === "remove") {
+    removeCommand(rest);
+    process.exit(0);
+  }
+
+  printUsageError(`Unknown command: ${command}`);
 } catch (error) {
   console.error(error.message);
   process.exit(1);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "architectonic",
-  "version": "0.0.3",
+  "version": "0.0.5",
   "description": "CLI for composing agentic system layers such as teleology, identity, project, and skills.",
   "license": "Apache-2.0",
   "type": "module",