@jstn-sdk/ma 0.1.13 → 0.14.0

package/bin/ma.js

@@ -1,20 +1,43 @@
 #!/usr/bin/env node
 
+import { spawnSync } from "node:child_process";
+import fs from "node:fs/promises";
+import path from "node:path";
+import { resolveAgentCommand } from "../src/agents.js";
 import { runBootstrap, runDoctor } from "../src/bootstrap.js";
 import { appendDecision } from "../src/decision-log.js";
-import { runCodex, shouldDelegateToCodex } from "../src/launcher.js";
+import { runAgent, shouldDelegateToCodex } from "../src/launcher.js";
+import { getRepoRoot, packageRoot } from "../src/paths.js";
 import {
   canMarkBuildDone,
   rejectsDirectProdPromotion,
   validateMergeTarget,
   validateReleaseOrigin,
 } from "../src/policy.js";
+import { choosePrelaunchInstall, installPrelaunchSelection } from "../src/prelaunch.js";
+import { executeGitOperation, inspectGitOperation } from "../src/release-operations.js";
 import { loadReleaseState } from "../src/release-state.js";
+import {
+  compileAgentIntegrations,
+  detectAgentEnvironments,
+  listAgentCompatAdapters,
+  validateAgentIntegrations,
+} from "../src/runtime/agent-compat.js";
 import { runExternalArchitectReview } from "../src/runtime/architect-review.js";
+import {
+  cancelAutonomousTask,
+  enqueueAutonomousTasks,
+  loadTaskQueue,
+  parseTaskInput,
+  runAutonomousTasks,
+} from "../src/runtime/autonomous-tasks.js";
 import { evaluateRuntimeBuildReadiness } from "../src/runtime/build-readiness.js";
 import { ingestCoreSources } from "../src/runtime/core-source-ingest.js";
+import { verifyLiveAgentMatrix } from "../src/runtime/live-agent-verification.js";
+import { createMaestroView, formatMaestroView } from "../src/runtime/maestro-output.js";
 import {
   appendObsidianOperationReceipt,
+  configureObsidianVault,
   createObsidianNote,
   deleteObsidianNote,
   listObsidianNotes,
@@ -23,7 +46,11 @@ import {
   writeObsidianVaultIndex,
 } from "../src/runtime/obsidian-integration-core.js";
 import { installObsidianPlugin } from "../src/runtime/obsidian-plugin-bridge.js";
+import { refreshProjectIndex } from "../src/runtime/project-context.js";
+import { purgeRedactionVault } from "../src/runtime/redaction-gateway.js";
 import { createRuntimeSummary, loadRuntimeSnapshot } from "../src/runtime/runtime-state.js";
+import { migrateSchemas } from "../src/runtime/schema-migrations.js";
+import { rollbackSetup } from "../src/setup-lifecycle.js";
 import {
   ensureSkillsInstalled,
   ensureSupportBundleInstalled,
@@ -42,46 +69,278 @@ import {
   runVibe,
 } from "../src/skills.js";
 import { syncStatusUpdates } from "../src/state-sync.js";
+import { renderReleaseGrid } from "../src/tui/status-grid.js";
 
 function printUsage() {
-  console.error("Secondary helper commands:");
-  console.error("  ma");
-  console.error("  ma bootstrap [--init-mcp]");
-  console.error("  ma doctor");
-  console.error("  ma setup");
-  console.error("  ma init");
-  console.error('  ma idea "..."');
-  console.error("  ma skills");
-  console.error("  ma core-ingest [--refresh]");
-  console.error("  ma obsidian-index [vault-path]");
-  console.error(
+  console.log("Meta-Architect CLI");
+  console.log("Usage: ma <command> [options]");
+  console.log("\nCommands:");
+  console.log("  ma");
+  console.log("  ma bootstrap [--init-mcp]");
+  console.log("  ma doctor [--json]");
+  console.log("  ma welcome");
+  console.log("  ma context refresh [--full|--json]");
+  console.log("  ma migrate [--dry-run|--rollback|--json]");
+  console.log("  ma setup [--obsidian-vault <path>]");
+  console.log("  first interactive launch: choose project or user scope and detected hosts");
+  console.log("  ma setup --rollback");
+  console.log("  ma setup --rollback --dry-run");
+  console.log("  ma uninstall");
+  console.log("  ma init");
+  console.log('  ma idea "..."');
+  console.log("  ma skills");
+  console.log("  ma core-ingest [--refresh]");
+  console.log("  ma agent-compat adapters|detect|compile|validate [path]");
+  console.log(
+    "  ma obsidian configure|list|read|create|update|delete|plugin-install [vault-path] [note-path] [content]",
+  );
+  console.log("  ma obsidian-index [vault-path]");
+  console.log(
     "  ma obsidian list|read|create|update|delete|plugin-install <vault-path> [note-path] [content]",
   );
-  console.error("  ma sdk-path");
-  console.error("  ma status [--maestro-view]");
-  console.error("  ma verify --architect");
-  console.error("  ma run $maestro|$arch|$sage|$flow|$vet|$vibe|$build [--auto-heal] [--parallel]");
-  console.error("  ma merge <source-branch> <target-branch>");
-  console.error("  ma release <origin-branch> <target-branch>");
+  console.log("  ma sdk-path");
+  console.log("  ma status [--maestro-view]");
+  console.log("  ma verify --architect|--agents-live [--json]");
+  console.log("  ma run $maestro|$arch|$sage|$flow|$vet|$vibe|$build [--auto-heal] [--parallel]");
+  console.log(
+    "  ma task add <goal> [--priority <level>] [--depends-on <id,...>] [--label <name>] [--deadline <ISO>]",
+  );
+  console.log("  ma task bulk <file|-> [--format json|yaml]");
+  console.log("  ma task list [--json]");
+  console.log("  ma task run [--concurrency <n>] [--max-tasks <n>] [--json]");
+  console.log("  ma task cancel <id> [reason]");
+  console.log("  ma hook active-autonomy|context-hydration");
+  console.log("  ma redaction purge [--dry-run]");
+  console.log("  ma merge <source-branch> <target-branch> [--dry-run|--execute]");
+  console.log("  ma release <origin-branch> <target-branch> [--dry-run|--execute]");
+}
+
+async function printVersion() {
+  const metadata = JSON.parse(await fs.readFile(path.join(packageRoot, "package.json"), "utf8"));
+  console.log(metadata.version);
+}
+
+function printCommandHelp(command) {
+  const help = {
+    setup: "ma setup [--json] [--obsidian-vault <path>] [--rollback] [--dry-run]",
+    doctor: "ma doctor [--json]",
+    status: "ma status [--json] [--maestro-view]",
+    context: "ma context refresh [--full] [--json]",
+    migrate: "ma migrate [--dry-run|--rollback] [--json]",
+    merge: "ma merge <source-branch> <target-branch> [--dry-run|--execute]",
+    release: "ma release <origin-branch> <target-branch> [--dry-run|--execute]",
+    "agent-compat": "ma agent-compat adapters|detect|compile|validate [path]",
+    verify: "ma verify --architect|--agents-live [--json]",
+    task: "ma task add|bulk|list|run|cancel ...",
+  };
+  console.log(help[command] ?? `No command-specific help is available for '${command}'.`);
+}
+
+function taskOption(rest, name) {
+  const value = getOptionValue(rest, name);
+  return value === undefined ? undefined : value;
+}
+
+async function runTaskCommand(rest) {
+  const action = rest[0] ?? "list";
+  if (action === "add") {
+    const flags = new Set([
+      "--priority",
+      "--depends-on",
+      "--label",
+      "--deadline",
+      "--id",
+      "--vendor",
+    ]);
+    const goal = rest
+      .slice(1)
+      .filter((value, index, values) => {
+        if (index > 0 && flags.has(values[index - 1])) return false;
+        return !value.startsWith("--") && !flags.has(value);
+      })
+      .join(" ");
+    if (!goal) throw new Error("Usage: ma task add <goal>");
+    const task = {
+      id: taskOption(rest, "--id"),
+      goal,
+      priority: taskOption(rest, "--priority"),
+      dependencies: taskOption(rest, "--depends-on")?.split(",").filter(Boolean),
+      labels: taskOption(rest, "--label")?.split(",").filter(Boolean),
+      deadline: taskOption(rest, "--deadline"),
+      vendor: taskOption(rest, "--vendor"),
+    };
+    const [added] = await enqueueAutonomousTasks(task);
+    console.log(
+      rest.includes("--json")
+        ? JSON.stringify(added, null, 2)
+        : `Queued ${added.id}: ${added.goal}`,
+    );
+    return;
+  }
+  if (action === "bulk") {
+    const source = rest[1];
+    if (!source) throw new Error("Usage: ma task bulk <file|-> [--format json|yaml]");
+    const raw =
+      source === "-"
+        ? await new Promise((resolve, reject) => {
+            const chunks = [];
+            process.stdin.on("data", (chunk) => chunks.push(chunk));
+            process.stdin.on("end", () => resolve(Buffer.concat(chunks).toString("utf8")));
+            process.stdin.on("error", reject);
+          })
+        : await fs.readFile(source, "utf8");
+    const format =
+      taskOption(rest, "--format") ??
+      (source.endsWith(".yaml") || source.endsWith(".yml") ? "yaml" : "json");
+    const added = await enqueueAutonomousTasks(await parseTaskInput(raw, format));
+    console.log(
+      rest.includes("--json") ? JSON.stringify(added, null, 2) : `Queued ${added.length} task(s)`,
+    );
+    return;
+  }
+  if (action === "list") {
+    const queue = await loadTaskQueue();
+    console.log(JSON.stringify(queue.tasks, null, 2));
+    return;
+  }
+  if (action === "cancel") {
+    if (!rest[1]) throw new Error("Usage: ma task cancel <id> [reason]");
+    const task = await cancelAutonomousTask(
+      rest[1],
+      rest
+        .slice(2)
+        .filter((value) => !value.startsWith("--"))
+        .join(" ") || undefined,
+    );
+    console.log(rest.includes("--json") ? JSON.stringify(task, null, 2) : `Cancelled ${task.id}`);
+    return;
+  }
+  if (action === "run") {
+    const result = await runAutonomousTasks({
+      concurrency: Number(taskOption(rest, "--concurrency") ?? 1),
+      maxTasks: Number(taskOption(rest, "--max-tasks") ?? Infinity),
+    });
+    if (rest.includes("--json")) console.log(JSON.stringify(result, null, 2));
+    else
+      console.log(
+        `Autonomous tasks: ${Object.entries(result.summary)
+          .map(([key, value]) => `${key}=${value}`)
+          .join(" ")}`,
+      );
+    if (result.summary.failed > 0 || result.summary.blocked > 0) process.exitCode = 1;
+    return;
+  }
+  throw new Error(`Unknown task action: ${action}`);
+}
+
+function getOptionValue(args, name) {
+  const index = args.indexOf(name);
+  return index === -1 ? undefined : args[index + 1];
+}
+
+function runHook(name) {
+  const scripts = {
+    "active-autonomy": "active-autonomy-hook.mjs",
+    "context-hydration": "context-hydration-hook.mjs",
+  };
+  const script = scripts[name];
+  if (!script) throw new Error(`Unknown hook: ${name}`);
+  const result = spawnSync(process.execPath, [path.join(packageRoot, "scripts", script)], {
+    cwd: process.cwd(),
+    env: process.env,
+    stdio: "inherit",
+  });
+  if (result.error) throw result.error;
+  process.exitCode = result.status ?? 1;
+}
+
+async function readObsidianContent(args, fallback) {
+  const filePath = getOptionValue(args, "--file");
+  if (filePath) return fs.readFile(filePath, "utf8");
+  if (args.includes("--stdin")) {
+    const chunks = [];
+    for await (const chunk of process.stdin) chunks.push(chunk);
+    return Buffer.concat(chunks).toString("utf8");
+  }
+  return fallback;
+}
+
+async function runAgentCompatCommand(rest) {
+  const [action = "adapters", firstArg, secondArg] = rest;
+  if (action === "adapters") {
+    console.log(JSON.stringify(listAgentCompatAdapters(), null, 2));
+    return;
+  }
+
+  if (action === "detect") {
+    console.log(JSON.stringify(await detectAgentEnvironments(firstArg ?? process.cwd()), null, 2));
+    return;
+  }
+
+  if (action === "validate") {
+    console.log(
+      JSON.stringify(await validateAgentIntegrations(firstArg ?? process.cwd()), null, 2),
+    );
+    return;
+  }
+
+  if (action === "compile") {
+    if (!firstArg) {
+      throw new Error("Usage: ma agent-compat compile <manifest.json> [output]");
+    }
+    const manifest = JSON.parse(await fs.readFile(firstArg, "utf8"));
+    const result = await compileAgentIntegrations(manifest, {
+      output: secondArg ?? process.cwd(),
+    });
+    console.log(JSON.stringify(result, null, 2));
+    if (!result.success) process.exitCode = 1;
+    return;
+  }
+
+  throw new Error(`Unknown Agent Compat action: ${action}`);
 }
 
-async function printStatus(releaseState) {
+async function printStatus(releaseState, { json = false } = {}) {
+  const runtimeSummary = createRuntimeSummary(await loadRuntimeSnapshot());
+  const evaluation = evaluateRuntimeBuildReadiness(releaseState, runtimeSummary);
+  const payload = {
+    schemaVersion: "0.1.0",
+    scope: "status",
+    release: releaseState,
+    runtime: runtimeSummary,
+    nextTriggers: evaluation.nextTriggers,
+  };
+  if (json) {
+    console.log(JSON.stringify(payload, null, 2));
+    return payload;
+  }
   console.log("Meta-Architect Status");
   console.log("=====================");
-  console.log(`Idea: ${releaseState.idea_status}`);
-  console.log(`Architecture: ${releaseState.architecture_status}`);
-  console.log(`Evidence: ${releaseState.evidence_status}`);
-  console.log(`Logic: ${releaseState.logic_status}`);
-  console.log(`Security: ${releaseState.security_status}`);
-  console.log(`Experience: ${releaseState.experience_status}`);
-  console.log(`Build: ${releaseState.build_status}`);
+  if (process.stdout.isTTY) {
+    console.log(renderReleaseGrid(releaseState, evaluation.nextTriggers));
+  }
+  if (process.stdout.isTTY) {
+    console.log(
+      `Core source snapshots: ${runtimeSummary.coreSourceIngestCount} (${runtimeSummary.coreSourceIngestStatus})`,
+    );
+    console.log(`Obsidian vault notes: ${runtimeSummary.obsidianVaultNoteCount}`);
+    console.log(`Obsidian CRUD receipts: ${runtimeSummary.obsidianVaultOperationCount}`);
+  }
+  if (!process.stdout.isTTY) {
+    console.log(`Idea: ${releaseState.idea_status}`);
+    console.log(`Architecture: ${releaseState.architecture_status}`);
+    console.log(`Evidence: ${releaseState.evidence_status}`);
+    console.log(`Logic: ${releaseState.logic_status}`);
+    console.log(`Security: ${releaseState.security_status}`);
+    console.log(`Experience: ${releaseState.experience_status}`);
+    console.log(`Build: ${releaseState.build_status}`);
 
-  const runtimeSummary = createRuntimeSummary(await loadRuntimeSnapshot());
-  console.log(
-    `Core source snapshots: ${runtimeSummary.coreSourceIngestCount} (${runtimeSummary.coreSourceIngestStatus})`,
-  );
-  console.log(`Obsidian vault notes: ${runtimeSummary.obsidianVaultNoteCount}`);
-  console.log(`Obsidian CRUD receipts: ${runtimeSummary.obsidianVaultOperationCount}`);
+    console.log(
+      `Core source snapshots: ${runtimeSummary.coreSourceIngestCount} (${runtimeSummary.coreSourceIngestStatus})`,
+    );
+    console.log(`Obsidian vault notes: ${runtimeSummary.obsidianVaultNoteCount}`);
+    console.log(`Obsidian CRUD receipts: ${runtimeSummary.obsidianVaultOperationCount}`);
+  }
   if (
     releaseState.build_status === "DONE" &&
     releaseState.merge_status !== "MERGED_TO_DEVELOPMENT"
@@ -90,7 +349,6 @@ async function printStatus(releaseState) {
     console.log("ma merge <feature/*> development");
     return;
   }
-  const evaluation = evaluateRuntimeBuildReadiness(releaseState, runtimeSummary);
   console.log("Next allowed triggers:");
   const triggers = evaluation.nextTriggers;
   if (triggers.length === 0) {
@@ -103,41 +361,11 @@ async function printStatus(releaseState) {
   }
 }
 
-async function printMaestroView() {
-  const snapshot = await loadRuntimeSnapshot();
-  const trackEntries = Object.entries(snapshot.maestroState.runtime_tracks);
-  console.log("Maestro View");
-  console.log("============");
-  console.log(`Global status: ${snapshot.maestroState.global_status}`);
-  console.log(`Orchestration id: ${snapshot.maestroState.orchestration_id ?? "not started"}`);
-  console.log("Runtime tracks:");
-  if (trackEntries.length === 0) {
-    console.log("- none");
-  } else {
-    for (const [trackId, track] of trackEntries) {
-      console.log(`- ${trackId}: ${track.active_gate} [${track.status}]`);
-      if (Array.isArray(track.blockers) && track.blockers.length > 0) {
-        console.log(`  blockers: ${track.blockers.join("; ")}`);
-      }
-    }
-  }
-
-  const lockEntries = Object.entries(snapshot.maestroState.downstream_lock_table);
-  console.log("Downstream locks:");
-  if (lockEntries.length === 0) {
-    console.log("- none");
-    return;
-  }
-
-  for (const [gate, lock] of lockEntries) {
-    console.log(`- ${gate}: ${lock.is_locked ? "locked" : "unlocked"}`);
-    if (Array.isArray(lock.locked_by) && lock.locked_by.length > 0) {
-      console.log(`  locked by: ${lock.locked_by.join(", ")}`);
-    }
-    if (lock.unlock_criteria) {
-      console.log(`  unlock criteria: ${lock.unlock_criteria}`);
-    }
-  }
+async function printMaestroView({ json = false, snapshot = null } = {}) {
+  const currentSnapshot = snapshot ?? (await loadRuntimeSnapshot());
+  const view = createMaestroView(currentSnapshot.maestroState);
+  if (json) return view;
+  process.stdout.write(formatMaestroView(view));
 }
 
 async function runBuild() {
@@ -177,7 +405,7 @@ async function runBuild() {
   console.log("Next step: ma merge <feature/*> development");
 }
 
-async function runMerge(sourceBranch, targetBranch) {
+async function runMerge(sourceBranch, targetBranch, mode = "approval") {
   const releaseState = await loadReleaseState();
 
   if (!validateMergeTarget(sourceBranch, targetBranch)) {
@@ -188,6 +416,25 @@ async function runMerge(sourceBranch, targetBranch) {
     throw new Error("Merge is blocked until build status is DONE");
   }
 
+  const operation = await inspectGitOperation(getRepoRoot(), sourceBranch, targetBranch);
+  if (!operation.available || !operation.sourceExists || !operation.clean) {
+    throw new Error(`Git preflight failed: ${operation.blockers.join("; ")}`);
+  }
+  if (mode === "dry-run") {
+    console.log(
+      `DRY RUN: approval state unchanged; would execute ${operation.display} on ${targetBranch}`,
+    );
+    return;
+  }
+  if (mode === "execute") {
+    if (operation.currentBranch !== targetBranch) {
+      throw new Error(
+        `Git execute requires current branch ${targetBranch}; found ${operation.currentBranch || "detached HEAD"}`,
+      );
+    }
+    await executeGitOperation(getRepoRoot(), operation);
+  }
+
   await appendDecision({
     kind: "merge",
     decision: `Merge approved from ${sourceBranch} to ${targetBranch}`,
@@ -201,10 +448,14 @@ async function runMerge(sourceBranch, targetBranch) {
     merge_status: "MERGED_TO_DEVELOPMENT",
   });
 
-  console.log(`Merge approved: ${sourceBranch} -> ${targetBranch}`);
+  console.log(
+    mode === "execute"
+      ? `Merge executed and approved: ${sourceBranch} -> ${targetBranch}`
+      : `Merge approved only: ${sourceBranch} -> ${targetBranch}; no Git command executed. Run \`${operation.display}\` explicitly or use --execute.`,
+  );
 }
 
-async function runRelease(originBranch, targetBranch) {
+async function runRelease(originBranch, targetBranch, mode = "approval") {
   const releaseState = await loadReleaseState();
 
   if (targetBranch !== "prod") {
@@ -221,6 +472,25 @@ async function runRelease(originBranch, targetBranch) {
     throw new Error("Release is blocked until merge_status is MERGED_TO_DEVELOPMENT");
   }
 
+  const operation = await inspectGitOperation(getRepoRoot(), originBranch, targetBranch);
+  if (!operation.available || !operation.sourceExists || !operation.clean) {
+    throw new Error(`Git preflight failed: ${operation.blockers.join("; ")}`);
+  }
+  if (mode === "dry-run") {
+    console.log(
+      `DRY RUN: approval state unchanged; would execute ${operation.display} on ${targetBranch}`,
+    );
+    return;
+  }
+  if (mode === "execute") {
+    if (operation.currentBranch !== targetBranch) {
+      throw new Error(
+        `Git execute requires current branch ${targetBranch}; found ${operation.currentBranch || "detached HEAD"}`,
+      );
+    }
+    await executeGitOperation(getRepoRoot(), operation);
+  }
+
   await appendDecision({
     kind: "release",
     decision: `Release approved from ${originBranch} to ${targetBranch}`,
@@ -234,7 +504,20 @@ async function runRelease(originBranch, targetBranch) {
     release_status: "SHIPPED_TO_PROD",
   });
 
-  console.log(`Release approved: ${originBranch} -> ${targetBranch}`);
+  console.log(
+    mode === "execute"
+      ? `Release executed and approved: ${originBranch} -> ${targetBranch}`
+      : `Release approved only: ${originBranch} -> ${targetBranch}; no Git command executed. Run \`${operation.display}\` explicitly or use --execute.`,
+  );
+}
+
+function resolveGitMode(args) {
+  const modes = [
+    args.includes("--dry-run") && "dry-run",
+    args.includes("--execute") && "execute",
+  ].filter(Boolean);
+  if (modes.length > 1) throw new Error("Choose only one of --dry-run or --execute");
+  return modes[0] ?? "approval";
 }
 
 async function main() {
@@ -242,40 +525,179 @@ async function main() {
   const args = process.argv.slice(2);
   const arg = rest[0];
 
+  if (args[0] === "--help" || args[0] === "-h" || args[0] === "help") {
+    if (args[0] === "help" && args[1]) printCommandHelp(args[1]);
+    else printUsage();
+    return;
+  }
+  if (args[0] === "--version" || args[0] === "-v" || args[0] === "version") {
+    await printVersion();
+    return;
+  }
+  if (args.includes("--help")) {
+    printCommandHelp(command);
+    return;
+  }
+
+  if (command === "hook") {
+    runHook(arg);
+    return;
+  }
+
+  if (command === "task") {
+    await runTaskCommand(rest);
+    return;
+  }
+
+  if (command === "redaction" && rest[0] === "purge") {
+    const result = await purgeRedactionVault({ dryRun: rest.includes("--dry-run") });
+    console.log(JSON.stringify(result, null, 2));
+    return;
+  }
+
   if (shouldDelegateToCodex(args)) {
-    await Promise.all([ensureSkillsInstalled(), ensureSupportBundleInstalled()]);
-    process.exitCode = runCodex(args);
+    const selection = await choosePrelaunchInstall();
+    const agentType = process.env.MA_AGENT || selection?.targets?.[0] || "codex";
+    if (selection) {
+      await installPrelaunchSelection(selection);
+    } else if (process.env.MA_AGENT) {
+      await installPrelaunchSelection({
+        schemaVersion: "0.1.0",
+        scope: "project",
+        targets: [agentType],
+      });
+    } else {
+      await Promise.all([ensureSkillsInstalled(), ensureSupportBundleInstalled()]);
+    }
+    if (!resolveAgentCommand(agentType)) {
+      console.log(
+        `Installed ${agentType} compatibility files; no executable host command is registered, so delegation was skipped.`,
+      );
+      return;
+    }
+    process.exitCode = runAgent(args, agentType);
     return;
   }
 
   if (command === "setup") {
-    const created = await runInit();
+    const jsonOutput = args.includes("--json");
+    if (args.includes("--rollback")) {
+      const result = await rollbackSetup(getRepoRoot(), { dryRun: args.includes("--dry-run") });
+      if (jsonOutput) console.log(JSON.stringify(result, null, 2));
+      else console.log(`${result.status}: ${result.removed.length} artifact(s) removed`);
+      return;
+    }
+    const report = await runInit({
+      refresh: args.includes("--refresh"),
+      obsidianVault: getOptionValue(args, "--obsidian-vault"),
+    });
+    if (
+      [...report.directories, ...report.files].some(
+        (entry) => entry.status === "warning" || entry.status === "warned" || entry.fatal === true,
+      )
+    ) {
+      process.exitCode = 1;
+    }
+    if (jsonOutput) {
+      console.log(JSON.stringify(report, null, 2));
+      return;
+    }
+
     console.log("meta-architect setup");
     console.log("====================");
-    for (const item of created) {
-      console.log(`ready: ${item}`);
+    for (const entry of [...report.directories, ...report.files]) {
+      const suffix = entry.warning ? `: ${entry.warning}` : "";
+      console.log(`${entry.status}: ${entry.path}${suffix}`);
+    }
+    for (const integration of report.integrations ?? []) {
+      console.log(`${integration.status}: ${integration.vaultPath}/${integration.notePath}`);
+    }
+    if (report.context) {
+      console.log(
+        `context: ${report.context.path} (${report.context.status}, ${report.context.completeness})`,
+      );
+      if (report.context.unknown.length > 0) {
+        console.log(`context unknown: ${report.context.unknown.join(", ")}`);
+      }
+    }
+    console.log("next: ma doctor | ma context refresh | ma setup --rollback");
+    return;
+  }
+
+  if (command === "welcome") {
+    const outcome = await runDoctor();
+    console.log("Meta-Architect welcome");
+    console.log("=======================");
+    console.log("Context: .ma/context/project-index.json");
+    console.log(
+      "Agents read: .ma/context/agent-brief.md, .ma/context/project-index.json, AGENTS.md",
+    );
+    console.log("Next: ma doctor | ma context refresh | ma setup --rollback");
+    process.exitCode = outcome.result === "BLOCKED" ? 1 : 0;
+    return;
+  }
+
+  if (command === "context" && rest[0] === "refresh") {
+    const result = await refreshProjectIndex(getRepoRoot(), {
+      mode: rest.includes("--full") ? "full" : "incremental",
+    });
+    const receipt = await fs.readFile(`${getRepoRoot()}/.ma/context/refresh-receipt.json`, "utf8");
+    if (rest.includes("--json")) console.log(receipt);
+    else {
+      console.log(`context refresh: ${result.freshness.status}`);
+      console.log(`changed: ${result.freshness.changedFiles.length}`);
+      console.log(`affected: ${JSON.parse(receipt).affectedArtifacts.join(", ") || "none"}`);
     }
     return;
   }
 
+  if (command === "uninstall") {
+    const result = await rollbackSetup(getRepoRoot());
+    console.log(JSON.stringify(result, null, 2));
+    return;
+  }
+
   if (command === "bootstrap") {
-    const outcome = await runBootstrap({ initMcp: rest.includes("--init-mcp") });
+    const outcome = await runBootstrap({
+      initMcp: rest.includes("--init-mcp"),
+      json: rest.includes("--json"),
+    });
+    if (rest.includes("--json")) console.log(JSON.stringify(outcome, null, 2));
     process.exitCode = outcome.result === "BLOCKED" ? 1 : 0;
     return;
   }
 
   if (command === "doctor") {
-    const outcome = await runDoctor();
+    const outcome = await runDoctor({ json: rest.includes("--json") });
+    if (rest.includes("--json")) console.log(JSON.stringify(outcome, null, 2));
     process.exitCode = outcome.result === "BLOCKED" ? 1 : 0;
     return;
   }
 
+  if (command === "migrate") {
+    const result = await migrateSchemas(getRepoRoot(), {
+      dryRun: rest.includes("--dry-run"),
+      rollback: rest.includes("--rollback"),
+    });
+    if (rest.includes("--json")) console.log(JSON.stringify(result, null, 2));
+    else
+      console.log(
+        `${result.status}: ${(result.migrated ?? result.restored ?? []).length} artifact(s)`,
+      );
+    process.exitCode = result.status === "failed" ? 1 : 0;
+    return;
+  }
+
   if (command === "init") {
-    const created = await runInit();
+    const report = await runInit({
+      refresh: args.includes("--refresh"),
+      obsidianVault: getOptionValue(args, "--obsidian-vault"),
+    });
     console.log("meta-architect init");
     console.log("===================");
-    for (const item of created) {
-      console.log(`ready: ${item}`);
+    for (const entry of [...report.directories, ...report.files]) {
+      const suffix = entry.warning ? `: ${entry.warning}` : "";
+      console.log(`${entry.status}: ${entry.path}${suffix}`);
     }
     return;
   }
@@ -309,13 +731,14 @@ async function main() {
     return;
   }
 
+  if (command === "agent-compat") {
+    await runAgentCompatCommand(rest);
+    return;
+  }
+
   if (command === "obsidian-index") {
-    const vaultPath = arg ?? process.env.MA_OBSIDIAN_VAULT;
-    if (!vaultPath) {
-      throw new Error("Obsidian vault path required: ma obsidian-index <vault-path>");
-    }
     await runInit();
-    const index = await writeObsidianVaultIndex({ vaultPath });
+    const index = await writeObsidianVaultIndex({ vaultPath: arg });
     console.log("Obsidian vault indexed");
     console.log(`Vault: ${index.vault_path}`);
     console.log(`Notes: ${index.note_count}`);
@@ -326,12 +749,17 @@ async function main() {
 
   if (command === "obsidian") {
     const [action, vaultPath, notePath, ...contentParts] = rest;
-    if (!action || !vaultPath) {
+    if (!action) {
       throw new Error(
         "Usage: ma obsidian list|read|create|update|delete|plugin-install <vault-path> [note-path] [content]",
       );
     }
     await runInit();
+    if (action === "configure") {
+      const config = await configureObsidianVault(vaultPath);
+      console.log(`Obsidian vault configured: ${config.vaultPath}`);
+      return;
+    }
     if (action === "plugin-install") {
       const receipt = await installObsidianPlugin({ vaultPath });
       await appendObsidianOperationReceipt({
@@ -368,10 +796,21 @@ async function main() {
       return;
     }
     if (action === "create") {
+      const content = await readObsidianContent(rest, contentParts.join(" "));
+      if (rest.includes("--dry-run")) {
+        console.log(
+          JSON.stringify(
+            { schemaVersion: "0.1.0", status: "would_create", notePath, content },
+            null,
+            2,
+          ),
+        );
+        return;
+      }
       const receipt = await createObsidianNote({
         vaultPath,
         notePath,
-        content: contentParts.join(" "),
+        content,
       });
       await appendObsidianOperationReceipt(receipt);
       await writeObsidianVaultIndex({ vaultPath });
@@ -379,10 +818,27 @@ async function main() {
       return;
     }
     if (action === "update") {
+      const content = await readObsidianContent(rest, contentParts.join(" "));
+      if (rest.includes("--dry-run")) {
+        const existing = await readObsidianNote({ vaultPath, notePath });
+        console.log(
+          JSON.stringify(
+            {
+              schemaVersion: "0.1.0",
+              status: existing.content === content ? "unchanged" : "would_update",
+              notePath,
+              content,
+            },
+            null,
+            2,
+          ),
+        );
+        return;
+      }
       const receipt = await updateObsidianNote({
         vaultPath,
         notePath,
-        content: contentParts.join(" "),
+        content,
       });
       await appendObsidianOperationReceipt(receipt);
       await writeObsidianVaultIndex({ vaultPath });
@@ -406,9 +862,23 @@ async function main() {
 
   if (command === "status") {
     const releaseState = await loadReleaseState();
-    await printStatus(releaseState);
-    if (rest.includes("--maestro-view")) {
-      await printMaestroView();
+    const json = rest.includes("--json");
+    const snapshot = rest.includes("--maestro-view") ? await loadRuntimeSnapshot() : null;
+    if (json && snapshot) {
+      const runtime = createRuntimeSummary(snapshot);
+      const evaluation = evaluateRuntimeBuildReadiness(releaseState, runtime);
+      const status = {
+        schemaVersion: "0.1.0",
+        scope: "status",
+        release: releaseState,
+        runtime,
+        nextTriggers: evaluation.nextTriggers,
+        maestro: createMaestroView(snapshot.maestroState),
+      };
+      process.stdout.write(`${JSON.stringify(status, null, 2)}\n`);
+    } else {
+      await printStatus(releaseState, { json });
+      if (snapshot) await printMaestroView({ snapshot });
     }
     return;
   }
@@ -425,15 +895,33 @@ async function main() {
     return;
   }
 
+  if (command === "verify" && rest.includes("--agents-live")) {
+    const report = await verifyLiveAgentMatrix({ cwd: process.cwd() });
+    if (rest.includes("--json")) {
+      process.stdout.write(`${JSON.stringify(report, null, 2)}\n`);
+    } else {
+      console.log(`Agent live verification: ${report.target_count} targets`);
+      console.log(`Runtime verified: ${report.runtime_verified}`);
+      console.log(`Distribution only: ${report.distribution_only}`);
+      console.log(`Blocked: ${report.blocked}`);
+      for (const result of report.results) {
+        console.log(
+          `- ${result.target}: ${result.status}${result.reason ? ` (${result.reason})` : ""}`,
+        );
+      }
+    }
+    return;
+  }
+
   if (command === "merge") {
-    const [sourceBranch, targetBranch] = rest;
-    await runMerge(sourceBranch, targetBranch);
+    const [sourceBranch, targetBranch] = rest.filter((arg) => !arg.startsWith("--"));
+    await runMerge(sourceBranch, targetBranch, resolveGitMode(rest));
     return;
   }
 
   if (command === "release") {
-    const [originBranch, targetBranch] = rest;
-    await runRelease(originBranch, targetBranch);
+    const [originBranch, targetBranch] = rest.filter((arg) => !arg.startsWith("--"));
+    await runRelease(originBranch, targetBranch, resolveGitMode(rest));
     return;
   }