fix: Encrypt secrets at rest with SOPS + age (#613)

- lib/env.sh: Two-tier secret loader (SOPS .env.enc > plaintext .env),
  remove ~/.netrc fallback
- bin/disinto: Add age key generation and SOPS encryption during init,
  remove write_netrc(), add `disinto secrets` subcommand (edit/show/migrate),
  add sops+age to preflight warnings
- .env.example: Annotate vars as [SECRET] or [CONFIG]
- .gitignore: Allow .env.enc and .sops.yaml to be committed
- BOOTSTRAP.md: Document SOPS + age setup, key backup, secret management
- AGENTS.md: Update AD-005 and coding conventions for .env.enc

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

.env.example

@@ -1,6 +1,12 @@
 # Disinto — Environment Configuration
 # Copy to .env and fill in your values.
 # NEVER commit .env to the repo.
+#
+# With SOPS + age installed, `disinto init` encrypts secrets into .env.enc
+# and removes plaintext .env. To migrate an existing .env: `disinto secrets migrate`
+#
+# Variables marked [SECRET] are credentials that grant access if leaked.
+# Variables marked [CONFIG] are non-sensitive and safe in plaintext.
 
 # ── Per-project config ────────────────────────────────────────────────────
 # Project-specific settings (FORGE_REPO, PROJECT_REPO_ROOT, PRIMARY_BRANCH,
@@ -8,23 +14,12 @@
 # for an example. Do NOT set them here; they leak into every session.
 
 # ── Forge (Forgejo) ─────────────────────────────────────────────────────
-# Base URL for the local Forgejo instance. disinto init provisions this.
+FORGE_URL=http://localhost:3000             # [CONFIG] local Forgejo instance
-FORGE_URL=http://localhost:3000
 
 # ── Auth tokens ───────────────────────────────────────────────────────────
-# Dev-agent token: push branches, create PRs, merge PRs.
+FORGE_TOKEN=                               # [SECRET] dev-bot API token
-# Use the dedicated bot account (e.g. dev-bot).
+FORGE_REVIEW_TOKEN=                        # [SECRET] review-bot API token
-# Branch protection: this account must be in the merge whitelist.
+FORGE_BOT_USERNAMES=                       # [CONFIG] comma-separated bot usernames
-FORGE_TOKEN=
-
-# Review-agent token: post review comments and submit formal approvals.
-# Use the review bot account (e.g. review-bot).
-# Branch protection: this account must be in the approvals whitelist.
-FORGE_REVIEW_TOKEN=
-
-# Comma-separated forge usernames to filter from issue comments.
-# The token owner is auto-detected; add extra bot accounts here if needed.
-FORGE_BOT_USERNAMES=
 
 # ── Backwards compatibility ───────────────────────────────────────────────
 # If CODEBERG_TOKEN is set but FORGE_TOKEN is not, env.sh falls back to
@@ -32,26 +27,25 @@ FORGE_BOT_USERNAMES=
 # CODEBERG_BOT_USERNAMES). No action needed for existing deployments.
 
 # ── Woodpecker CI ─────────────────────────────────────────────────────────
-WOODPECKER_TOKEN=
+WOODPECKER_TOKEN=                          # [SECRET] Woodpecker API token
-WOODPECKER_SERVER=http://localhost:8000
+WOODPECKER_SERVER=http://localhost:8000     # [CONFIG] Woodpecker server URL
 # WOODPECKER_REPO_ID — now per-project, set in projects/*.toml [ci] section
 
 # Woodpecker Postgres (for direct DB queries)
-WOODPECKER_DB_PASSWORD=
+WOODPECKER_DB_PASSWORD=                    # [SECRET] Postgres password
-WOODPECKER_DB_USER=woodpecker
+WOODPECKER_DB_USER=woodpecker              # [CONFIG] Postgres user
-WOODPECKER_DB_HOST=127.0.0.1
+WOODPECKER_DB_HOST=127.0.0.1              # [CONFIG] Postgres host
-WOODPECKER_DB_NAME=woodpecker
+WOODPECKER_DB_NAME=woodpecker              # [CONFIG] Postgres database name
 
 # ── Matrix (optional — real-time notifications & escalation replies) ──────
-MATRIX_HOMESERVER=http://localhost:8008     # Dendrite/Synapse URL
+MATRIX_HOMESERVER=http://localhost:8008     # [CONFIG] Dendrite/Synapse URL
-MATRIX_BOT_USER=@factory:your.server       # bot's Matrix user ID
+MATRIX_BOT_USER=@factory:your.server       # [CONFIG] bot's Matrix user ID
-MATRIX_TOKEN=                              # bot's access token
+MATRIX_TOKEN=                              # [SECRET] bot's access token
-MATRIX_ROOM_ID=                            # coordination room ID (!xxx:your.server)
+MATRIX_ROOM_ID=                            # [CONFIG] coordination room ID
 
 # ── Project-specific secrets ──────────────────────────────────────────────
 # Store all project secrets here so formulas reference env vars, never hardcode.
-# Example: BASE_RPC_URL for on-chain evolution scripts.
+BASE_RPC_URL=                              # [SECRET] on-chain RPC endpoint
-BASE_RPC_URL=
 
 # ── Tuning ────────────────────────────────────────────────────────────────
-CLAUDE_TIMEOUT=7200                        # max seconds per Claude invocation
+CLAUDE_TIMEOUT=7200                        # [CONFIG] max seconds per Claude invocation

.gitignore

@@ -1,6 +1,10 @@
-# Secrets
+# Plaintext secrets (never commit)
 .env
 
+# Encrypted secrets — safe to commit (.env.enc is SOPS-encrypted)
+!.env.enc
+!.sops.yaml
+
 # Per-box project config (generated by disinto init)
 projects/*.toml
 

AGENTS.md

@@ -50,7 +50,7 @@ disinto/
 - All scripts start with `#!/usr/bin/env bash` and `set -euo pipefail`
 - Source shared environment: `source "$(dirname "$0")/../lib/env.sh"`
 - Log to `$LOGFILE` using the `log()` function from env.sh or defined locally
-- Never hardcode secrets — all come from `.env` or TOML project files
+- Never hardcode secrets — all come from `.env.enc` (or `.env` fallback) or TOML project files
 - Never embed secrets in issue bodies, PR descriptions, or comments — use env var references (e.g. `$BASE_RPC_URL`)
 - ShellCheck must pass (CI runs `shellcheck` on all `.sh` files)
 - Avoid duplicate code — shared helpers go in `lib/`
@@ -129,7 +129,7 @@ Humans write these. Agents read and enforce them.
 | AD-002 | Single-threaded pipeline per project. | One dev issue at a time. No new work while a PR awaits CI or review. Prevents merge conflicts and keeps context clear. |
 | AD-003 | The runtime creates and destroys, the formula preserves. | Runtime manages worktrees/sessions/temp. Formulas commit knowledge to git before signaling done. |
 | AD-004 | Event-driven > polling > fixed delays. | Never `waitForTimeout` or hardcoded sleep. Use phase files, webhooks, or poll loops with backoff. |
-| AD-005 | Secrets via env var indirection, never in issue bodies. | Issue bodies become code. Secrets go in `.env` or TOML project files, referenced as `$VAR_NAME`. |
+| AD-005 | Secrets via env var indirection, never in issue bodies. | Issue bodies become code. Secrets go in `.env.enc` (SOPS-encrypted) or fall back to `.env`, referenced as `$VAR_NAME`. |
 
 **Who enforces what:**
 - **Gardener** checks open backlog issues against ADs during grooming; closes violations with a comment referencing the AD number.

BOOTSTRAP.md

@@ -31,7 +31,39 @@ This will:
 
 No external accounts or tokens needed.
 
-## 1. Configure `.env`
+## 1. Secret Management (SOPS + age)
+
+Disinto encrypts secrets at rest using [SOPS](https://github.com/getsops/sops) with [age](https://age-encryption.org/) encryption. When `sops` and `age` are installed, `disinto init` automatically:
+
+1. Generates an age key at `~/.config/sops/age/keys.txt` (if none exists)
+2. Creates `.sops.yaml` pinning the age public key
+3. Encrypts all secrets into `.env.enc` (safe to commit)
+4. Removes the plaintext `.env`
+
+**Install the tools:**
+
+```bash
+# age (key generation)
+apt install age          # Debian/Ubuntu
+brew install age         # macOS
+
+# sops (encryption/decryption)
+# Download from https://github.com/getsops/sops/releases
+```
+
+**The age private key** at `~/.config/sops/age/keys.txt` is the single file that must be protected. Back it up securely — without it, `.env.enc` cannot be decrypted. LUKS disk encryption on the VPS protects this key at rest.
+
+**Managing secrets after setup:**
+
+```bash
+disinto secrets edit     # Opens .env.enc in $EDITOR, re-encrypts on save
+disinto secrets show     # Prints decrypted secrets (for debugging)
+disinto secrets migrate  # Converts existing plaintext .env -> .env.enc
+```
+
+**Fallback:** If `sops`/`age` are not installed, `disinto init` writes secrets to a plaintext `.env` file with a warning. All agents load secrets transparently — `lib/env.sh` checks for `.env.enc` first, then falls back to `.env`.
+
+## 2. Configure `.env`
 
 ```bash
 cp .env.example .env
@@ -70,7 +102,7 @@ CLAUDE_TIMEOUT=7200                   # seconds per Claude invocation
 
 If you have an existing deployment using `CODEBERG_TOKEN` / `REVIEW_BOT_TOKEN` in `.env`, those still work — `env.sh` falls back to the old names automatically. No migration needed.
 
-## 2. Configure Project TOML
+## 3. Configure Project TOML
 
 Each project needs a `projects/<name>.toml` file with box-specific settings
 (absolute paths, Woodpecker CI IDs, Matrix credentials, forge URL). These files are
@@ -98,7 +130,7 @@ forge_url       = "http://localhost:3000"
 The repo ships `projects/*.toml.example` templates showing the expected
 structure. See any `.toml.example` file for the full field reference.
 
-## 3. Claude Code Global Settings
+## 4. Claude Code Global Settings
 
 Configure `~/.claude/settings.json` with **only** permissions and `skipDangerousModePermissionPrompt`. Do not add hooks to the global settings — `agent-session.sh` injects per-worktree hooks automatically.
 
@@ -124,7 +156,7 @@ claude --dangerously-skip-permissions
 # Exit after it initializes successfully
 ```
 
-## 4. File Ownership
+## 5. File Ownership
 
 Everything under `/home/debian` must be owned by `debian:debian`. Root-owned files cause permission errors when agents run as the `debian` user.
 
@@ -139,7 +171,7 @@ Verify no root-owned files exist in agent temp directories:
 find /tmp/dev-* /tmp/harb-* /tmp/review-* -not -user debian 2>/dev/null
 ```
 
-## 4b. Woodpecker CI + Forgejo Integration
+## 5b. Woodpecker CI + Forgejo Integration
 
 `disinto init` automatically configures Woodpecker to use the local Forgejo instance as its forge backend if `WOODPECKER_SERVER` is set in `.env`. This includes:
 
@@ -184,7 +216,7 @@ curl -X POST \
 
 Woodpecker will now trigger pipelines on pushes to Forgejo and push commit status back. Disinto queries Woodpecker directly for CI status (with a forge API fallback), so pipeline results are visible even if Woodpecker's status push to Forgejo is delayed.
 
-## 5. Prepare the Target Repo
+## 6. Prepare the Target Repo
 
 ### Required: CI pipeline
 
@@ -268,7 +300,7 @@ entire repo as "new", generating a noisy first-run diff.
 
 See `formulas/run-planner.toml` (agents-update step) for the full AGENTS.md conventions.
 
-## 6. Write Good Issues
+## 7. Write Good Issues
 
 Dev-agent works best with issues that have:
 
@@ -283,7 +315,7 @@ Dev-agent works best with issues that have:
 
 Dev-agent checks that all referenced issues are closed (= merged) before starting work. If any are open, the issue is skipped and checked again next cycle.
 
-## 7. Install Cron
+## 8. Install Cron
 
 ```bash
 crontab -e
@@ -342,7 +374,7 @@ FACTORY_ROOT=/home/you/disinto
 
 The staggered offsets prevent agents from competing for resources. Each project gets its own lock file (`/tmp/dev-agent-{name}.lock`) derived from the `name` field in its TOML, so concurrent runs across projects are safe.
 
-## 8. Verify
+## 9. Verify
 
 ```bash
 # Should complete with "all clear" (no problems to fix)
@@ -363,7 +395,7 @@ tail -30 dev/dev-agent.log
 tail -30 review/review.log
 ```
 
-## 9. Optional: Matrix Notifications
+## 10. Optional: Matrix Notifications
 
 If you want real-time notifications and human-in-the-loop escalation:
 

bin/disinto

@@ -5,6 +5,7 @@
 # Commands:
 #   disinto init <repo-url> [options]   Bootstrap a new project
 #   disinto status                      Show factory status
+#   disinto secrets <edit|show|migrate> Manage encrypted secrets
 #
 # Usage:
 #   disinto init https://github.com/user/repo
@@ -25,6 +26,7 @@ disinto — autonomous code factory CLI
 Usage:
   disinto init <repo-url> [options]    Bootstrap a new project
   disinto status                       Show factory status
+  disinto secrets <edit|show|migrate>  Manage encrypted secrets (.env.enc)
 
 Init options:
   --branch <name>      Primary branch (default: auto-detect)
@@ -62,26 +64,73 @@ clone_url_from_slug() {
   printf '%s/%s.git' "$forge_url" "$slug"
 }
 
-# Write (or update) credentials in ~/.netrc for a given host.
+# Ensure an age key exists; generate one if missing.
-write_netrc() {
+# Exports AGE_PUBLIC_KEY on success.
-  local host="$1" login="$2" token="$3"
+ensure_age_key() {
-  local netrc="${HOME}/.netrc"
+  local key_dir="${HOME}/.config/sops/age"
+  local key_file="${key_dir}/keys.txt"
 
-  # Remove existing entry for this host if present
+  if [ -f "$key_file" ]; then
-  if [ -f "$netrc" ]; then
+    AGE_PUBLIC_KEY="$(age-keygen -y "$key_file" 2>/dev/null)"
-    local tmp
+    export AGE_PUBLIC_KEY
-    tmp=$(mktemp)
+    return 0
-    awk -v h="$host" '
-      $0 ~ "^machine " h { skip=1; next }
-      /^machine / { skip=0 }
-      !skip
-    ' "$netrc" > "$tmp"
-    mv "$tmp" "$netrc"
   fi
 
-  # Append new entry
+  if ! command -v age-keygen &>/dev/null; then
-  printf 'machine %s\nlogin %s\npassword %s\n' "$host" "$login" "$token" >> "$netrc"
+    return 1
-  chmod 600 "$netrc"
+  fi
+
+  mkdir -p "$key_dir"
+  age-keygen -o "$key_file" 2>/dev/null
+  chmod 600 "$key_file"
+  AGE_PUBLIC_KEY="$(age-keygen -y "$key_file" 2>/dev/null)"
+  export AGE_PUBLIC_KEY
+  echo "Generated age key: ${key_file}"
+}
+
+# Write .sops.yaml pinning the age recipient for .env.enc files.
+write_sops_yaml() {
+  local pub_key="$1"
+  cat > "${FACTORY_ROOT}/.sops.yaml" <<EOF
+creation_rules:
+  - path_regex: \.env\.enc$
+    age: "${pub_key}"
+EOF
+}
+
+# Encrypt a dotenv file to .env.enc using SOPS + age.
+# Usage: encrypt_env_file <input> <output>
+encrypt_env_file() {
+  local input="$1" output="$2"
+  sops -e --input-type dotenv --output-type dotenv "$input" > "$output"
+}
+
+# Store secrets into .env.enc (encrypted) if SOPS + age available, else .env (plaintext).
+# Reads existing .env, updates/adds vars, writes back.
+write_secrets_encrypted() {
+  local env_file="${FACTORY_ROOT}/.env"
+  local enc_file="${FACTORY_ROOT}/.env.enc"
+
+  if command -v sops &>/dev/null && command -v age-keygen &>/dev/null; then
+    if ensure_age_key; then
+      # Write .sops.yaml if missing
+      if [ ! -f "${FACTORY_ROOT}/.sops.yaml" ]; then
+        write_sops_yaml "$AGE_PUBLIC_KEY"
+      fi
+
+      # Encrypt the plaintext .env to .env.enc
+      if [ -f "$env_file" ]; then
+        encrypt_env_file "$env_file" "$enc_file"
+        rm -f "$env_file"
+        echo "Secrets encrypted to .env.enc (plaintext .env removed)"
+        return 0
+      fi
+    fi
+  fi
+
+  # Fallback: keep plaintext .env
+  echo "Warning: sops/age not available — secrets stored in plaintext .env" >&2
+  return 0
 }
 
 FORGEJO_DATA_DIR="${HOME}/.disinto/forgejo"
@@ -385,6 +434,14 @@ preflight_check() {
   if ! command -v docker &>/dev/null; then
     echo "Warning: docker not found (needed for Forgejo provisioning)" >&2
   fi
+  if ! command -v sops &>/dev/null; then
+    echo "Warning: sops not found (secrets will be stored in plaintext .env)" >&2
+    echo "  Install: https://github.com/getsops/sops/releases" >&2
+  fi
+  if ! command -v age-keygen &>/dev/null; then
+    echo "Warning: age not found (needed for secret encryption with SOPS)" >&2
+    echo "  Install: apt install age  /  brew install age" >&2
+  fi
 
   if [ "$errors" -gt 0 ]; then
     echo "" >&2
@@ -836,6 +893,9 @@ p.write_text(text)
   # Install cron jobs
   install_cron "$project_name" "$toml_path" "$auto_yes"
 
+  # Encrypt secrets if SOPS + age are available
+  write_secrets_encrypted
+
   echo ""
   echo "Done. Project ${project_name} is ready."
   echo "  Config:  ${toml_path}"
@@ -919,11 +979,64 @@ with open(sys.argv[1], 'rb') as f:
   fi
 }
 
+# ── secrets command ────────────────────────────────────────────────────────────
+
+disinto_secrets() {
+  local subcmd="${1:-}"
+  local enc_file="${FACTORY_ROOT}/.env.enc"
+  local env_file="${FACTORY_ROOT}/.env"
+
+  case "$subcmd" in
+    edit)
+      if [ ! -f "$enc_file" ]; then
+        echo "Error: ${enc_file} not found. Run 'disinto secrets migrate' first." >&2
+        exit 1
+      fi
+      sops "$enc_file"
+      ;;
+    show)
+      if [ ! -f "$enc_file" ]; then
+        echo "Error: ${enc_file} not found." >&2
+        exit 1
+      fi
+      sops -d "$enc_file"
+      ;;
+    migrate)
+      if [ ! -f "$env_file" ]; then
+        echo "Error: ${env_file} not found — nothing to migrate." >&2
+        exit 1
+      fi
+      if ! command -v sops &>/dev/null || ! command -v age-keygen &>/dev/null; then
+        echo "Error: sops and age are required for migration." >&2
+        echo "  Install sops: https://github.com/getsops/sops/releases" >&2
+        echo "  Install age:  apt install age  /  brew install age" >&2
+        exit 1
+      fi
+      if ! ensure_age_key; then
+        echo "Error: failed to generate age key" >&2
+        exit 1
+      fi
+      if [ ! -f "${FACTORY_ROOT}/.sops.yaml" ]; then
+        write_sops_yaml "$AGE_PUBLIC_KEY"
+        echo "Created: .sops.yaml"
+      fi
+      encrypt_env_file "$env_file" "$enc_file"
+      rm -f "$env_file"
+      echo "Migrated: .env -> .env.enc (plaintext removed)"
+      ;;
+    *)
+      echo "Usage: disinto secrets <edit|show|migrate>" >&2
+      exit 1
+      ;;
+  esac
+}
+
 # ── Main dispatch ────────────────────────────────────────────────────────────
 
 case "${1:-}" in
-  init)   shift; disinto_init "$@" ;;
+  init)    shift; disinto_init "$@" ;;
-  status) shift; disinto_status "$@" ;;
+  status)  shift; disinto_status "$@" ;;
+  secrets) shift; disinto_secrets "$@" ;;
   -h|--help) usage ;;
   *)         usage ;;
 esac

lib/env.sh

@@ -7,8 +7,12 @@ set -euo pipefail
 # Resolve script root (parent of lib/)
 FACTORY_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
 
-# Load .env if present
+# Load secrets: prefer .env.enc (SOPS-encrypted), fall back to plaintext .env
-if [ -f "$FACTORY_ROOT/.env" ]; then
+if [ -f "$FACTORY_ROOT/.env.enc" ] && command -v sops &>/dev/null; then
+  set -a
+  eval "$(sops -d --output-type dotenv "$FACTORY_ROOT/.env.enc" 2>/dev/null)" || true
+  set +a
+elif [ -f "$FACTORY_ROOT/.env" ]; then
   set -a
   # shellcheck source=/dev/null
   source "$FACTORY_ROOT/.env"
@@ -24,13 +28,10 @@ if [ -n "${PROJECT_TOML:-}" ] && [ -f "$PROJECT_TOML" ]; then
   source "${FACTORY_ROOT}/lib/load-project.sh" "$PROJECT_TOML"
 fi
 
-# Forge token: new FORGE_TOKEN > legacy CODEBERG_TOKEN > ~/.netrc
+# Forge token: new FORGE_TOKEN > legacy CODEBERG_TOKEN
 if [ -z "${FORGE_TOKEN:-}" ]; then
   FORGE_TOKEN="${CODEBERG_TOKEN:-}"
 fi
-if [ -z "${FORGE_TOKEN:-}" ]; then
-  FORGE_TOKEN="$(awk '/codeberg.org/{getline;getline;print $2}' ~/.netrc 2>/dev/null || true)"
-fi
 export FORGE_TOKEN
 export CODEBERG_TOKEN="${FORGE_TOKEN}"  # backwards compat