Merge pull request #985 from coleam00/dev

Release 0.3.0

Author: Wirasm

CHANGELOG.md

@@ -7,6 +7,39 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.3.0] - 2026-04-08
+
+Env-leak gate hardening, SSE reliability fixes, isolation cleanup smarter merge detection, build/version improvements, and deploy hardening.
+
+### Added
+
+- **Env-leak gate (target repo `.env` keys)**: scan auto-loaded `.env` filenames for 7 sensitive keys (`ANTHROPIC_API_KEY`, `OPENAI_API_KEY`, etc.) and refuse to register or spawn into a codebase whose `.env` would silently re-inject keys into Claude/Codex subprocesses. Default is fail-closed (`allow_env_keys = false`). Includes a per-codebase consent column, registration gate, pre-spawn check in both Claude and Codex clients, and a 422 API error with web UI checkbox (#1036).
+- **CLI `--allow-env-keys` flag** for `archon workflow run` — grant env-leak-gate consent during auto-registration without needing the Web UI. Audit-logged as `env_leak_consent_granted` with `actor: 'user-cli'` (#973, #983).
+- **Global `allow_target_repo_keys` flag** in `~/.archon/config.yaml` — bypass the env-leak gate for all codebases on this machine. Per-repo `.archon/config.yaml` `allow_target_repo_keys: false` re-enables the gate for that repo. The server emits `env_leak_gate_disabled` once per process per source the first time `loadConfig` resolves the bypass as active (#973, #983).
+- **`PATCH /api/codebases/:id`** endpoint to flip `allow_env_keys` on existing codebases without delete/re-add. Audit-logged at `warn` level on every grant and revoke, including a `scanStatus` field that distinguishes "scanned" from "scan failed" so audit reviewers can tell empty key lists apart (#973, #983).
+- **Settings → Projects per-row toggle** to grant or revoke env-key consent retroactively, with an "env keys allowed" badge and inline error feedback if the PATCH fails (#973, #983).
+- **Startup env-leak scan**: when `allow_target_repo_keys` is not set, the server emits one `startup_env_leak_gate_will_block` warn per registered codebase whose `.env` would block the next spawn. Skipped entirely when the global bypass is active (#973, #983).
+- **Squash-merge and PR-merge detection** for `isolation cleanup --merged`. Unions three signals (ancestry via `git branch --merged`, patch equivalence via `git cherry`, and PR state via `gh`) to safely clean up worktrees whose branches were squash-merged. Adds `--include-closed` flag to also remove worktrees whose PRs were closed without merging (#1027).
+- **Git commit hash in `archon version`** output. Read at runtime via `git rev-parse` in dev or from a build-time constant in compiled binaries; falls back to `unknown` (#1035).
+
+### Changed
+
+- **Env-leak gate error messages** are now context-aware: separate remediation copy for Web Add-Project, CLI auto-register, and pre-spawn-of-existing-codebase paths. Previously every error pointed at the Web UI checkbox even from the CLI (#973, #983).
+- **SSE event buffer TTL** raised from 3s to 60s and capacity from 50 to 500 events, fixing dropped `tool_result` events during the 5s reconnect grace window that left tool cards perpetually spinning. Cleanup timer now resets on each new event so the buffer is held for TTL past the most recent event, not the first one. Buffer overflow and TTL expiration now log at `warn` level for observability (#1037).
+- **Binary build detection** moved from runtime env sniffing (`import.meta.dir` / `process.execPath`) to a build-time `BUNDLED_IS_BINARY` constant in `@archon/paths`. Logger uses `pino-pretty` as a destination stream on the main thread instead of a worker-thread transport, eliminating the `require.resolve('pino-pretty')` lookup that crashed inside Bun's `$bunfs` virtual filesystem in compiled binaries. Same code path runs in dev and binaries — no environment detection (#982).
+- **Cloud-init deployment script** hardened: dedicated `archon` user (docker group, no sudo) with SSH keys copied from the default cloud user, 2GB swapfile to prevent OOM during docker build on small VPSes, `ufw allow 443/tcp` and `443/udp` for HTTP/3 QUIC, fail-fast on network errors, and clearer setup-complete messaging (#981).
+
+### Fixed
+
+- **Env-leak gate worktree path lookup**: pre-spawn consent check now falls back to `findCodebaseByPathPrefix()` when the exact path lookup misses, so workflow runs in `.../worktrees/feature-branch` correctly inherit consent from the source codebase (#1036).
+- **`EnvLeakError` FATAL classification** in the workflow executor now checks `error.name === 'EnvLeakError'` directly instead of pattern-matching the message, immune to message rewording (#1036).
+- **Scanner unreadable-file handling**: distinguishes `ENOENT` (skip) from `EACCES` and other errors so unreadable `.env` files surface as findings instead of silently bypassing the gate (#1036).
+
+### Security
+
+- The default `allow_env_keys` per codebase is `false` (fail-closed). Codebases with sensitive keys in their auto-loaded `.env` files (`ANTHROPIC_API_KEY`, `OPENAI_API_KEY`, etc.) are blocked at the next workflow run. **Remediation paths** (any one): (1) remove the key from `.env`, (2) rename to `.env.secrets`, (3) toggle "Allow env keys" in Settings → Projects, (4) `archon workflow run --allow-env-keys ...`, (5) set `allow_target_repo_keys: true` in `~/.archon/config.yaml`. See `docs/reference/security.md` for full details (#1036, #973, #983).
+
+
 ## [0.2.12] - 2026-03-20
 
 Chat-first navigation redesign, DAG graph viewer, per-node MCP and skills, and extensive bug fixes across the web UI and workflow engine.

CLAUDE.md

@@ -198,6 +198,10 @@ bun run cli workflow run implement --branch feature-auth "Add auth"
 # Opt out of isolation (run in live checkout)
 bun run cli workflow run quick-fix --no-worktree "Fix typo"
 
+# Grant env-leak-gate consent during auto-registration (for repos whose .env
+# contains sensitive keys). Audit-logged with actor: 'user-cli'.
+bun run cli workflow run plan --cwd /path/to/leaky/repo --allow-env-keys "..."
+
 # Show running workflows
 bun run cli workflow status
 
@@ -224,6 +228,9 @@ bun run cli isolation cleanup 14  # Custom days
 # Clean up environments with branches merged into main (also deletes remote branches)
 bun run cli isolation cleanup --merged
 
+# Also remove environments with closed (abandoned) PRs
+bun run cli isolation cleanup --merged --include-closed
+
 # Validate workflow definitions and their referenced resources
 bun run cli validate workflows              # All workflows
 bun run cli validate workflows my-workflow  # Single workflow
@@ -740,6 +747,12 @@ Pattern: Use `classifyIsolationError()` (from `@archon/isolation`) to map git er
 - `POST /api/workflows/runs/{runId}/abandon` - Abandon a non-terminal run (marks as cancelled)
 - `DELETE /api/workflows/runs/{runId}` - Delete a terminal workflow run and its events
 
+**Codebases:**
+- `GET /api/codebases` / `GET /api/codebases/:id` - List / fetch codebases
+- `POST /api/codebases` - Register a codebase (clone or local path); body accepts `allowEnvKeys` for the env-leak gate
+- `PATCH /api/codebases/:id` - Flip the `allow_env_keys` consent bit; body: `{ allowEnvKeys: boolean }`. Audit-logged at `warn` level on every grant/revoke (`env_leak_consent_granted` / `env_leak_consent_revoked`) with `codebaseId`, `path`, `files`, `keys`, `scanStatus`, `actor`
+- `DELETE /api/codebases/:id` - Delete a codebase and clean up resources
+
 **Artifact Files:**
 - `GET /api/artifacts/:runId/*` - Serve a workflow artifact file by run ID and relative path; returns `text/markdown` for `.md` files, `text/plain` otherwise; 400 on path traversal (`..`), 404 if run or file not found
 

bun.lock

@@ -6,20 +6,30 @@
 #
 # Paste this into your VPS provider's "User Data" field when creating a server.
 # Tested on: Ubuntu 22.04+, Debian 12+
+# Works with any cloud-init compatible provider (DigitalOcean, Hetzner, Linode,
+# Vultr, AWS EC2, Hostinger, etc.)
 #
 # What this does:
 #   1. Installs Docker + Docker Compose plugin
 #   2. Opens firewall ports (SSH, HTTP, HTTPS)
-#   3. Clones the repo to /opt/archon
-#   4. Prepares .env and Caddyfile from examples
-#   5. Builds the Docker image (~5 min)
+#   3. Creates a 2GB swapfile (helps small VPS builds avoid OOM)
+#   4. Clones the repo to /opt/archon
+#   5. Prepares .env and Caddyfile from examples
+#   6. Creates a dedicated 'archon' user (docker group only, no sudo)
+#   7. Builds the Docker image (~5 min) as the archon user
 #
-# After the server boots (~5-8 min), SSH in and:
+# Note: On VPS with <2GB RAM, the docker build step can OOM without swap.
+# Note: The 'archon' user has docker access but NOT sudo. For administrative
+#       tasks (updates, reboots), use the default cloud user or root.
+#
+# After the server boots (~5-8 min), SSH in as the archon user:
+#   ssh archon@your-server-ip
 #   1. Edit /opt/archon/.env — set your AI credentials, DOMAIN, DATABASE_URL
 #   2. cd /opt/archon && docker compose --profile with-db --profile cloud up -d
 #   3. Open https://your-domain.com
 #
 # IMPORTANT: Before starting, point your domain's DNS A record to this server's IP.
+#           SSH keys from the default cloud user are copied to 'archon'.
 #
 
 package_update: true
@@ -30,29 +40,66 @@ packages:
   - git
   - ufw
 
+users:
+  - default
+  - name: archon
+    gecos: Archon Service User
+    shell: /bin/bash
+    lock_passwd: true
+
 runcmd:
+  # --- Swap (helps small VPS avoid OOM during docker build) ---
+  - |
+    if [ ! -f /swapfile ]; then
+      fallocate -l 2G /swapfile || dd if=/dev/zero of=/swapfile bs=1M count=2048
+      chmod 600 /swapfile
+      mkswap /swapfile
+      swapon /swapfile
+      echo '/swapfile none swap sw 0 0' >> /etc/fstab
+    fi
+
   # --- Docker ---
   - curl -fsSL https://get.docker.com | sh
-  - systemctl enable docker
-  - systemctl start docker
+  - usermod -aG docker archon
 
-  # --- Firewall ---
+  # --- Copy SSH keys from default user to archon (so login works immediately) ---
+  - |
+    DEFAULT_USER=$(getent passwd 1000 | cut -d: -f1)
+    if [ -n "$DEFAULT_USER" ] && [ -f /home/$DEFAULT_USER/.ssh/authorized_keys ]; then
+      mkdir -p /home/archon/.ssh
+      cp /home/$DEFAULT_USER/.ssh/authorized_keys /home/archon/.ssh/authorized_keys
+      chmod 700 /home/archon/.ssh
+      chmod 600 /home/archon/.ssh/authorized_keys
+      chown -R archon:archon /home/archon/.ssh
+    elif [ -f /root/.ssh/authorized_keys ]; then
+      mkdir -p /home/archon/.ssh
+      cp /root/.ssh/authorized_keys /home/archon/.ssh/authorized_keys
+      chmod 700 /home/archon/.ssh
+      chmod 600 /home/archon/.ssh/authorized_keys
+      chown -R archon:archon /home/archon/.ssh
+    fi
+
+  # --- Firewall (443/udp needed for HTTP/3 QUIC via Caddy) ---
   - ufw allow 22/tcp
   - ufw allow 80/tcp
-  - ufw allow 443
+  - ufw allow 443/tcp
+  - ufw allow 443/udp
   - ufw --force enable
 
-  # --- Clone and configure ---
-  - git clone https://github.com/coleam00/Archon.git /opt/archon
-  - cp /opt/archon/.env.example /opt/archon/.env
-  - cp /opt/archon/Caddyfile.example /opt/archon/Caddyfile
+  # --- Clone and configure (fail fast — single shell so set -e applies) ---
+  - |
+    set -e
+    git clone https://github.com/coleam00/Archon.git /opt/archon
+    cp /opt/archon/.env.example /opt/archon/.env
+    cp /opt/archon/Caddyfile.example /opt/archon/Caddyfile
+    chown -R archon:archon /opt/archon
 
-  # --- Pre-pull external images ---
-  - docker pull postgres:17-alpine
-  - docker pull caddy:2-alpine
+  # --- Pre-pull external images (as archon, via docker group) ---
+  - sudo -u archon docker pull postgres:17-alpine
+  - sudo -u archon docker pull caddy:2-alpine
 
-  # --- Build the app image ---
-  - cd /opt/archon && docker compose build
+  # --- Build the app image as archon ---
+  - sudo -u archon -H bash -c 'cd /opt/archon && docker compose build'
 
   # --- Signal completion ---
   - |
@@ -61,6 +108,13 @@ runcmd:
     Archon server setup complete!
     ============================================
 
+    Log in as the 'archon' user (not root):
+      ssh archon@<server-ip>
+
+    Note: the 'archon' user has docker access but no sudo. For system
+    maintenance (apt upgrade, reboots), log in as the default cloud user
+    or root.
+
     Next steps:
 
       1. Edit credentials and domain:
@@ -85,7 +139,7 @@ runcmd:
 
     Logs:     docker compose logs -f
     Health:   curl https://your-domain.com/api/health
-    Docs:     https://github.com/coleam00/Archon/blob/main/docs/docker.md
+    Docs:     https://archon.diy/deployment/docker/
     ============================================
     DONE
   - echo "[archon] Setup complete. Edit /opt/archon/.env and run docker compose up."

deploy/cloud-init.yml

@@ -30,6 +30,7 @@ CREATE TABLE IF NOT EXISTS remote_agent_codebases (
   repository_url VARCHAR(500),
   default_cwd VARCHAR(500) NOT NULL,
   ai_assistant_type VARCHAR(20) DEFAULT 'claude',
+  allow_env_keys BOOLEAN NOT NULL DEFAULT FALSE,
   commands JSONB DEFAULT '{}'::jsonb,
   created_at TIMESTAMP DEFAULT NOW(),
   updated_at TIMESTAMP DEFAULT NOW()
@@ -307,3 +308,7 @@ ALTER TABLE remote_agent_conversations
 -- From migration 016: ended_reason on sessions
 ALTER TABLE remote_agent_sessions
   ADD COLUMN IF NOT EXISTS ended_reason TEXT;
+
+-- From migration 021: allow_env_keys on codebases
+ALTER TABLE remote_agent_codebases
+  ADD COLUMN IF NOT EXISTS allow_env_keys BOOLEAN NOT NULL DEFAULT FALSE;

migrations/000_combined.sql

@@ -0,0 +1,4 @@
+-- Add per-codebase consent bit for subprocess .env key leakage
+-- DEFAULT FALSE = safe by default; user must explicitly opt in
+ALTER TABLE remote_agent_codebases
+  ADD COLUMN allow_env_keys BOOLEAN NOT NULL DEFAULT FALSE;

migrations/021_add_allow_env_keys_to_codebases.sql

@@ -1,6 +1,6 @@
 {
   "name": "archon",
-  "version": "0.2.13",
+  "version": "0.3.0",
   "private": true,
   "workspaces": [
     "packages/*"

package.json

@@ -127,6 +127,9 @@ Options:
   --json                     Output machine-readable JSON (for workflow list)
   --workflow <name>          Workflow to run for 'continue' (default: archon-assist)
   --no-context               Skip context injection for 'continue'
+  --allow-env-keys           Grant env-key consent during auto-registration
+                             (bypasses the env-leak gate for this codebase;
+                             logs an audit entry)
 
 Examples:
   archon chat "What does the orchestrator do?"
@@ -190,6 +193,7 @@ async function main(): Promise<number> {
         reason: { type: 'string' },
         workflow: { type: 'string' },
         'no-context': { type: 'boolean' },
+        'allow-env-keys': { type: 'boolean' },
       },
       allowPositionals: true,
       strict: false, // Allow unknown flags to pass through
@@ -211,6 +215,7 @@ async function main(): Promise<number> {
   const resumeFlag = values.resume as boolean | undefined;
   const spawnFlag = values.spawn as boolean | undefined;
   const jsonFlag = values.json as boolean | undefined;
+  const allowEnvKeysFlag = values['allow-env-keys'] as boolean | undefined;
 
   // Handle help flag
   if (values.help) {
@@ -323,6 +328,7 @@ async function main(): Promise<number> {
               fromBranch,
               noWorktree,
               resume: resumeFlag,
+              allowEnvKeys: allowEnvKeysFlag,
               quiet: values.quiet as boolean | undefined,
               verbose: values.verbose as boolean | undefined,
             };
@@ -459,7 +465,8 @@ async function main(): Promise<number> {
             // Check for --merged flag in remaining args
             const mergedFlag = args.includes('--merged') || positionals.includes('--merged');
             if (mergedFlag) {
-              await isolationCleanupMergedCommand();
+              const includeClosed = args.includes('--include-closed');
+              await isolationCleanupMergedCommand({ includeClosed });
             } else {
               const days = parseInt(positionals[2] ?? '7', 10);
               await isolationCleanupCommand(days);

packages/cli/src/cli.ts

@@ -2,7 +2,7 @@
  * Tests for isolation complete command
  */
 import { describe, it, expect, beforeEach, afterEach, mock, spyOn } from 'bun:test';
-import { isolationCompleteCommand } from './isolation';
+import { isolationCompleteCommand, isolationCleanupMergedCommand } from './isolation';
 
 const mockLogger = {
   fatal: mock(() => undefined),
@@ -44,6 +44,27 @@ mock.module('@archon/core/services/cleanup-service', () => ({
   cleanupMergedWorktrees: mockCleanupMergedWorktrees,
 }));
 
+const mockListEnvironments = mock(() =>
+  Promise.resolve({
+    codebases: [
+      {
+        codebaseId: 'cb-1',
+        defaultCwd: '/test/repo',
+        repositoryUrl: 'https://github.com/owner/repo',
+        environments: [],
+      },
+    ],
+    totalEnvironments: 0,
+    ghostsReconciled: 0,
+  })
+);
+const mockCleanupMergedEnvironments = mock(() => Promise.resolve({ removed: [], skipped: [] }));
+
+mock.module('@archon/core/operations/isolation-operations', () => ({
+  listEnvironments: mockListEnvironments,
+  cleanupMergedEnvironments: mockCleanupMergedEnvironments,
+}));
+
 const mockHasUncommittedChanges = mock(() => Promise.resolve(false));
 // Default: gh returns empty PR array, git log returns empty string (no commits to report)
 const mockExecFileAsync = mock((cmd: string) =>
@@ -358,3 +379,32 @@ describe('isolationCompleteCommand', () => {
     expect(consoleLogSpy).toHaveBeenCalledWith('\nComplete: 1 completed, 1 failed, 1 not found');
   });
 });
+
+describe('isolationCleanupMergedCommand', () => {
+  let consoleLogSpy: ReturnType<typeof spyOn>;
+  let consoleErrorSpy: ReturnType<typeof spyOn>;
+
+  beforeEach(() => {
+    consoleLogSpy = spyOn(console, 'log').mockImplementation(() => {});
+    consoleErrorSpy = spyOn(console, 'error').mockImplementation(() => {});
+    mockCleanupMergedEnvironments.mockReset();
+    mockCleanupMergedEnvironments.mockResolvedValue({ removed: [], skipped: [] });
+  });
+
+  afterEach(() => {
+    consoleLogSpy.mockRestore();
+    consoleErrorSpy.mockRestore();
+  });
+
+  it('passes includeClosed=true when --include-closed flag is set', async () => {
+    await isolationCleanupMergedCommand({ includeClosed: true });
+    expect(mockCleanupMergedEnvironments).toHaveBeenCalledWith('cb-1', '/test/repo', {
+      includeClosed: true,
+    });
+  });
+
+  it('defaults to includeClosed=false', async () => {
+    await isolationCleanupMergedCommand();
+    expect(mockCleanupMergedEnvironments).toHaveBeenCalledWith('cb-1', '/test/repo', {});
+  });
+});