feat: consolidate daemon/autonomous into squads run (#587)

.github/workflows/ci.yml

@@ -180,3 +180,22 @@ jobs:
 
       - name: Run npm-install smoke test
         run: bash scripts/e2e-smoke.sh
+
+  docker-e2e:
+    name: Docker E2E (clean env gate)
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '22'
+          cache: 'npm'
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Run Docker E2E test
+        run: bash scripts/e2e-docker.sh

package.json

@@ -27,6 +27,7 @@
     "test": "vitest run",
     "test:watch": "vitest",
     "test:coverage": "vitest run --coverage",
+    "test:docker": "bash scripts/e2e-docker.sh",
     "prepublishOnly": "npm run build"
   },
   "keywords": [

scripts/e2e-docker.sh

@@ -0,0 +1,92 @@
+#!/usr/bin/env bash
+# E2E Docker test: builds a clean Ubuntu container, installs squads-cli from
+# tarball (like a real user), and runs smoke tests inside it.
+#
+# Catches issues that local tests miss:
+# - Missing files in npm package
+# - Broken bin entry / shebang
+# - Node version incompatibilities
+# - Permission issues (non-root user)
+# - Missing runtime dependencies
+#
+# Usage: bash scripts/e2e-docker.sh
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(cd "$SCRIPT_DIR/.." && pwd)"
+DOCKERFILE="$REPO_ROOT/test/e2e/Dockerfile.first-run"
+IMAGE_NAME="squads-cli-e2e"
+
+echo "▶ Building package..."
+cd "$REPO_ROOT"
+npm run build
+
+echo "▶ Packing tarball..."
+TARBALL=$(npm pack --quiet)
+TARBALL_PATH="$REPO_ROOT/$TARBALL"
+
+cleanup() {
+  echo "▶ Cleaning up..."
+  rm -f "$TARBALL_PATH"
+  docker rmi "$IMAGE_NAME" 2>/dev/null || true
+}
+trap cleanup EXIT
+
+echo "▶ Building Docker image (clean Ubuntu + squads-cli from tarball)..."
+docker build \
+  -f "$DOCKERFILE" \
+  --build-arg "TARBALL=$TARBALL" \
+  -t "$IMAGE_NAME" \
+  "$REPO_ROOT"
+
+echo "▶ Running tests inside container..."
+docker run --rm "$IMAGE_NAME" bash -c '
+set -euo pipefail
+
+step() { echo ""; echo "=== STEP: $1 ==="; }
+
+step "squads --version"
+squads --version
+
+step "squads --help"
+squads --help | head -20
+
+step "squads init --yes --force"
+mkdir -p /tmp/test-project && cd /tmp/test-project
+git init -q && git commit --allow-empty -q -m "init"
+squads init --yes --force
+
+step "squads status"
+squads status
+
+step "squads run --status (daemon status)"
+squads run --status
+
+step "squads run --dry-run --once (autopilot preview)"
+squads run --dry-run --once || true
+
+step "squads run company --dry-run (single squad preview)"
+squads run company --dry-run || true
+
+step "squads run --pause \"e2e test\""
+squads run --pause "e2e test"
+
+step "squads run --status (should show paused)"
+squads run --status
+
+step "squads run --resume"
+squads run --resume
+
+step "squads run --status (should show not running)"
+squads run --status
+
+step "squads autonomous status (deprecated alias)"
+squads autonomous status || true
+
+step "squads doctor"
+squads doctor || true
+
+echo ""
+echo "✅ All Docker E2E tests passed"
+'

scripts/scrub-secrets.sh

@@ -0,0 +1,97 @@
+#!/usr/bin/env bash
+# ─────────────────────────────────────────────────────────────────────
+# Git history secret scrub for squads-cli (PUBLIC REPO)
+#
+# Removes leaked secrets from git history using git-filter-repo.
+# This rewrites history — all collaborators must re-clone after.
+#
+# Prerequisites:
+#   brew install git-filter-repo   (or pip install git-filter-repo)
+#
+# What gets scrubbed:
+#   1. Telemetry API key (base64-encoded)
+#   2. Telemetry endpoint URL (base64-encoded)
+#   3. Local DB credentials (two connection strings)
+#
+# Usage:
+#   1. Review this script
+#   2. Run: bash scripts/scrub-secrets.sh
+#   3. Verify: git log -p --all -S '<pattern>' should return nothing
+#   4. Force push: git push --force --all && git push --force --tags
+# ─────────────────────────────────────────────────────────────────────
+
+set -euo pipefail
+
+REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+cd "$REPO_ROOT"
+
+# Preflight
+if ! command -v git-filter-repo &>/dev/null; then
+  echo "ERROR: git-filter-repo not found"
+  echo "Install: brew install git-filter-repo"
+  exit 1
+fi
+
+# Safety: must be on a clean working tree
+if [ -n "$(git status --porcelain)" ]; then
+  echo "ERROR: Working tree not clean. Commit or stash changes first."
+  exit 1
+fi
+
+echo "=== Strings to scrub from git history ==="
+echo ""
+echo "1. Telemetry API key (base64):     c3FfdGVsX3YxXzdmOGE5YjJjM2Q0ZTVmNmE="
+echo "2. Telemetry endpoint (base64):    aHR0cHM6Ly9zcXVhZHMtdGVsZW1ldHJ5LTk3ODg3MTgxNzYxMC51cy1jZW50cmFsMS5ydW4uYXBwL3Bpbmc="
+echo "3. DB credential 1:               postgresql://user:password@localhost:5432/squads"
+echo "4. DB credential 2:               postgresql://squads:squads_local_dev@localhost:5433/squads"
+echo ""
+echo "This will REWRITE git history. All collaborators must re-clone."
+echo ""
+read -p "Continue? (yes/no): " CONFIRM
+if [ "$CONFIRM" != "yes" ]; then
+  echo "Aborted."
+  exit 0
+fi
+
+# Create the replacements file
+REPLACEMENTS=$(mktemp)
+cat > "$REPLACEMENTS" <<'REPLACE'
+c3FfdGVsX3YxXzdmOGE5YjJjM2Q0ZTVmNmE===>REDACTED_TELEMETRY_KEY
+aHR0cHM6Ly9zcXVhZHMtdGVsZW1ldHJ5LTk3ODg3MTgxNzYxMC51cy1jZW50cmFsMS5ydW4uYXBwL3Bpbmc===>REDACTED_TELEMETRY_ENDPOINT
+postgresql://user:password@localhost:5432/squads==>REDACTED_DB_URL
+postgresql://squads:squads_local_dev@localhost:5433/squads==>REDACTED_DB_URL
+REPLACE
+
+echo "▶ Running git-filter-repo with blob replacements..."
+git filter-repo --replace-text "$REPLACEMENTS" --force
+
+rm -f "$REPLACEMENTS"
+
+echo ""
+echo "=== Verification ==="
+echo ""
+
+# Verify scrub worked
+FOUND=0
+for pattern in "c3FfdGVsX3YxXzdm" "aHR0cHM6Ly9zcXVhZHMtdGVsZW1ldHJ5" "user:password@localhost" "squads_local_dev"; do
+  HITS=$(git log --all -p | grep -c "$pattern" 2>/dev/null || true)
+  if [ "$HITS" -gt 0 ]; then
+    echo "FAIL: '$pattern' still found $HITS time(s)"
+    FOUND=1
+  else
+    echo "OK:   '$pattern' scrubbed"
+  fi
+done
+
+echo ""
+if [ "$FOUND" -eq 0 ]; then
+  echo "All secrets scrubbed from git history."
+  echo ""
+  echo "Next steps:"
+  echo "  1. git push --force --all"
+  echo "  2. git push --force --tags"
+  echo "  3. Tell collaborators to re-clone (git pull won't work after rewrite)"
+  echo "  4. Rotate the telemetry API key server-side (if not already done)"
+else
+  echo "WARNING: Some secrets still found. Manual investigation needed."
+fi

src/cli.ts

@@ -53,7 +53,7 @@ import { applyStackConfig } from './lib/stack-config.js';
 // Register-pattern commands (must define subcommand structure before parseAsync)
 import { registerOrchestrateCommand } from './commands/orchestrate.js';
 import { registerTriggerCommand } from './commands/trigger.js';
-import { registerAutonomousCommand } from './commands/autonomous.js';
+// autonomous.ts removed — daemon lifecycle consolidated into run-modes.ts
 import { registerApprovalCommand } from './commands/approval.js';
 import { registerDeployCommand } from './commands/deploy.js';
 import { registerEvalCommand } from './commands/eval.js';
@@ -303,6 +303,10 @@ program
   .option('--once', 'Autopilot: run one cycle then exit')
   .option('--phased', 'Autopilot: use dependency-based phase ordering (from SQUAD.md depends_on)')
   .option('--no-eval', 'Skip post-run COO evaluation')
+  .option('--stop', 'Stop running daemon')
+  .option('--status', 'Show daemon status, running agents, next routines')
+  .option('--pause [reason]', 'Pause daemon without stopping')
+  .option('--resume', 'Resume daemon after pause')
   .addHelpText('after', `
 Examples:
   $ squads run engineering              Run squad conversation (lead → scan → work → review)
@@ -316,9 +320,13 @@ Examples:
   $ squads run engineering -w           Run in background but tail logs
   $ squads run research --provider=google  Use Gemini CLI instead of Claude
   $ squads run engineering/issue-solver --cloud  Dispatch to cloud worker
-  $ squads run                          Autopilot mode (watch → decide → dispatch → learn)
-  $ squads run --once --dry-run         Preview one autopilot cycle
-  $ squads run -i 15 --budget 50       Autopilot: 15min cycles, $50/day cap
+  $ squads run                          Daemon mode (cron routines + scoring + dispatch)
+  $ squads run --once --dry-run         Preview one cycle then exit
+  $ squads run -i 15 --budget 50       Custom: 15min cycles, $50/day cap
+  $ squads run --status                 Show daemon status and next routines
+  $ squads run --stop                   Stop running daemon
+  $ squads run --pause "quota"          Pause daemon without stopping
+  $ squads run --resume                 Resume after pause
 `)
   .action(async (target, options) => {
     const { runCommand } = await import('./commands/run.js');
@@ -711,7 +719,7 @@ program
 program
   .command('autopilot')
   .alias('daemon')
-  .description('[deprecated] Use "squads run" instead — autopilot mode when no target given')
+  .description('[deprecated] Use "squads run" instead — unified daemon mode')
   .option('-i, --interval <minutes>', 'Minutes between cycles', '30')
   .option('-p, --parallel <count>', 'Max parallel agent runs', '2')
   .option('-b, --budget <dollars>', 'Max daily spend in dollars (0 = unlimited/subscription)', '0')
@@ -898,8 +906,41 @@ registerTriggerCommand(program);
 // Approval command group - human-in-the-loop for agents
 registerApprovalCommand(program);
 
-// Autonomous command group - scheduled routines
-registerAutonomousCommand(program);
+// Autonomous command — deprecated, now `squads run --status/--stop/--pause/--resume`
+program
+  .command('autonomous')
+  .alias('auto')
+  .description('[deprecated] Daemon lifecycle moved to squads run flags')
+  .argument('[action]', 'start|stop|status|pause|resume')
+  .argument('[reason]', 'Pause reason (optional)')
+  .action(async (action?: string, reason?: string) => {
+    const colors = termColors;
+    const mapping: Record<string, string> = {
+      start: 'squads run',
+      stop: 'squads run --stop',
+      status: 'squads run --status',
+      pause: 'squads run --pause',
+      resume: 'squads run --resume',
+    };
+    const newCmd = mapping[action || 'status'] || 'squads run --status';
+    writeLine(`  ${colors.yellow}Note: "squads autonomous ${action || ''}" is now "${newCmd}"${termReset}`);
+    writeLine();
+
+    const { runCommand } = await import('./commands/run.js');
+    switch (action) {
+      case 'start':
+        return runCommand(null, {});
+      case 'stop':
+        return runCommand(null, { stop: true });
+      case 'pause':
+        return runCommand(null, { pause: reason || 'Manual pause' });
+      case 'resume':
+        return runCommand(null, { resume: true });
+      case 'status':
+      default:
+        return runCommand(null, { status: true });
+    }
+  });
 
 // ─── System ──────────────────────────────────────────────────────────────────
 
@@ -1076,7 +1117,7 @@ program
 
 program.command('stack', { hidden: true }).description('[removed]').action(removedCommand('stack', 'Infrastructure is managed via the cloud. Use: squads login'));
 program.command('cron', { hidden: true }).description('[removed]').action(removedCommand('cron', 'Use platform scheduler: squads trigger list'));
-program.command('tonight', { hidden: true }).description('[removed]').action(removedCommand('tonight', 'Use platform scheduler for overnight runs: squads autonomous start'));
+program.command('tonight', { hidden: true }).description('[removed]').action(removedCommand('tonight', 'Use: squads run (daemon mode, no arguments)'));
 program.command('live', { hidden: true }).description('[removed]').action(removedCommand('live', 'Use: squads dash'));
 program.command('top', { hidden: true }).description('[removed]').action(removedCommand('top', 'Use: squads sessions'));
 program.command('watch', { hidden: true }).description('[removed]').action(removedCommand('watch', 'Use: watch -n 2 squads status'));