secret-handling-runtime

Decision aid for how a system handles secrets during operation: in memory, in pipes, in scratch files, in error messages, in logs, in process tables. Use when designing or reviewing any code that touches secret material at runtime.

This skill complements the existing addons/security/secure-token-load.md (which covers tokens at rest — file modes, heredoc patterns, source locations). This skill covers runtime — what happens to those secrets between load and use, and what happens when something fails mid-operation.

Triggers

• "secret in env" / "SECRETS_ENV"
• "shred" / "tmpfs" / "scratch surface"
• "set -e" / "error trap" / "ERR EXIT"
• "fd passing" / "named pipe for secrets"
• "log scrubbing" / "secret in error message"
• "ps aux" / "/proc/self/environ"
• "memory wipe" / "zeroize"

---

Section 1: File-descriptor / named-pipe passing

Suggested default — one secret per fd

# Caller
encrypt_program 3<<<"$SECRET_VALUE" 4<<<"$OTHER_SECRET" arg1 arg2

# Inside encrypt_program
secret=$(cat <&3)
other=$(cat <&4)
# fd 3 and fd 4 are open for the duration of the program
# never appear in /proc/self/environ, never in `ps aux`

Why this beats env vars:

• env, printenv, /proc/<pid>/environ are readable by other processes on most systems
• Env vars persist across exec chains (subprocess inherits)
• set -x (bash trace) prints env values for each subprocess invocation
• Crash dumps include env

Anti-pattern: SECRETS_ENV aggregation (review M3)

# WRONG
SECRETS_ENV="api_key=$KEY1;db_pwd=$KEY2;jwt_secret=$KEY3"
some_program  # all three secrets visible to any process inspecting environ

Single variable = single leak vector. If set -x fires, all three leak. If a child process logs env, all three leak. Use one fd per secret OR one named pipe per secret.

Named pipes (mkfifo) when fd passing isn't structural

mkfifo /tmp/secrets.fifo
chmod 600 /tmp/secrets.fifo
{ echo "$SECRET" > /tmp/secrets.fifo; } &
program /tmp/secrets.fifo
rm /tmp/secrets.fifo

Caveats:

• /tmp/ should be tmpfs (Section 2)
• Named pipes are visible to other users via ls -la /tmp/; use a per-process directory in /run/<uid>/ or /dev/shm/ that's mode 700

---

Section 2: Scratch surface — tmpfs only

Suggested default — refuse to operate if /tmp is not tmpfs

require_tmpfs() {
    local path="${1:-/tmp}"
    if ! mountpoint -q "$path" || \
       [ "$(findmnt -no FSTYPE "$path")" != "tmpfs" ]; then
        echo "ERROR: $path is not tmpfs; refusing to operate" >&2
        exit 1
    fi
}
require_tmpfs /tmp

Why tmpfs only:

• tmpfs is RAM-resident; on shutdown, contents are gone
• Disk-backed /tmp (some servers, some embedded systems) leaves traces in flash wear-leveling, journal, and swap
• shred -u on flash storage is worse than nothing — it gives false assurance against wear-leveling reality (review M1)

shred is not a substitute

shred overwrites file content multiple times then deletes. On flash storage (SSD, USB, eMMC), the wear-leveling layer remaps writes to fresh blocks; the original data sits in unmapped blocks until eventual reuse. shred -u deletes the visible file but the data remains recoverable via filesystem forensics.

shred IS appropriate for spinning disks where the OS guarantees in-place rewrites — uncommon in 2026.

For ephemeral scratch, tmpfs is the answer. For persistent encrypted storage, the encryption (LUKS, FileVault) is the answer; never write secrets to "ordinary" disk and try to delete them later.

Documenting the scratch surface

## Scratch surface

| Path | Backing | Acceptable for secrets? |
|------|---------|-------------------------|
| /tmp | tmpfs (verified at start) | yes |
| /var/tmp | disk | NO — refuse to write secrets |
| /dev/shm | tmpfs | yes |
| ~/.cache | disk | NO |

---

Section 3: Error-path safety in shell

Suggested default — set -euo pipefail + trap cleanup

#!/bin/bash
set -euo pipefail

cleanup() {
    # zeroize what we can; unmount tmpfs scratch
    [ -n "${SCRATCH_DIR:-}" ] && [ -d "$SCRATCH_DIR" ] && \
        shred -u "$SCRATCH_DIR"/*.tmp 2>/dev/null
    [ -n "${SECRET_VAR:-}" ] && unset SECRET_VAR
    [ -n "${MOUNTED:-}" ] && umount "$MOUNTED" 2>/dev/null
}
trap cleanup ERR EXIT INT TERM

# ... actual script logic

Without set -e, a failing openssl enc or cat mid-pipeline can produce a partial-state file the next step processes (review M2). Without the trap, an interrupted script leaves secret-bearing scratch files intact.

Specific shell pitfalls

Issue	Mitigation
set -e doesn't fire inside if/while/&&/|| chains	Test exit codes explicitly in those contexts: if foo; then ...; else echo "foo failed"; exit 1; fi
set -e ignores failures in subshells unless caller checks	(...) returns the subshell's exit; check it
set -x (debug) prints expanded variables — including secrets	Never enable set -x on secret-bearing code paths; use set +x defensively before secret handling
cat /etc/secret | openssl enc ... — pipe failures partial-write	set -o pipefail to make the pipeline return any failure

Python / Node / Go equivalents

Language	Pattern
Python	try/finally for cleanup; subprocess.run(..., check=True); secrets.compare_digest for any constant-time compare
Node	try/finally + process.on('exit', cleanup); pass-fd via child_process.spawn(..., { stdio: [...] })
Go	defer cleanup(); os/exec.Cmd.ExtraFiles for fd passing

---

Section 4: Memory hygiene

When to bother

In long-running processes (daemons, sessions), wipe key material from memory after use:

// C with libsodium
sodium_memzero(key, sizeof(key));

# Python — limited; CPython doesn't guarantee zeroization but bytearrays help
import ctypes
key = bytearray(32)
# ... use key
ctypes.memset(ctypes.addressof(ctypes.c_char.from_buffer(key)), 0, len(key))

For short-lived programs (one-shot scripts), explicit zeroization is mostly performative — the process exits, OS reclaims memory. The bigger concern is:

• Don't put secrets in long-lived globals; make them function-local
• Don't pass secrets as positional command-line args (ps aux reveals them)
• Don't log secrets, even to debug

mlock to prevent swap

mlock(key_buffer, key_size);
// ... use
sodium_memzero(key_buffer, key_size);
munlock(key_buffer, key_size);

mlock prevents the page from being swapped to disk. Required when the process may run on a system with swap enabled. libsodium's sodium_mlock/sodium_munlock is portable.

---

Section 5: Identifier hygiene

Anti-pattern: serial numbers, IDs in metadata files (review L2)

{
  "yk5_serial": "12345678",
  "bio_serial": "87654321"
}

Hardware serials in metadata expose:

• Operator identity (serials are often issued to specific people)
• Hardware revisions (different firmware = different attack surface)
• Inventory enumeration (attacker who recovers .meta.json learns what other devices the operator carries)

Remediation: salted hash

import hashlib, secrets
salt = secrets.token_bytes(16)  # per-USB, stored alongside
yk5_hash = hashlib.sha256(salt + yk5_serial.encode()).hexdigest()
# .meta.json stores yk5_hash and salt; serial is never persisted

The salt is stored with the metadata, so loss of the metadata file reveals nothing. The hash lets you verify "is this the right key?" without revealing which key.

Apply broadly

The pattern applies to:

• Hardware serials (USB, YubiKey, smart card, TPM EK)
• Email addresses, usernames in stored audit
• IP addresses in long-term logs
• Build host fingerprints in artifact manifests

If you need to identify-without-revealing, salted-hash. If you need to compare-without-revealing, HMAC with a per-context key.

---

Section 6: LUKS / full-disk header hygiene

Required pattern (review M5)

# Provisioning
cryptsetup luksHeaderBackup /dev/sdX --header-backup-file /secure/headers/sdX.luksheader
gpg --encrypt --recipient hq-pubkey /secure/headers/sdX.luksheader
# Store encrypted backup off-device

# Recovery (when header is corrupted)
cryptsetup luksHeaderRestore /dev/sdX --header-backup-file /secure/headers/sdX.luksheader

A single bad block in the LUKS header bricks the volume. Backups are non-negotiable for production. The backup is encrypted to an HQ key (not the operator's keys) so its loss doesn't compromise active sessions and its theft doesn't compromise active sessions either — restoration requires HQ.

---

Section 7: Logging policy

Default

• Never log secret material, even truncated, even in debug, even in error
• Log secret-bearing operation events with public metadata only (who, when, where, success/fail — not what)
• Log retention: secret-bearing systems should keep logs short and rotate aggressively; logs are themselves a secondary attack surface

Examples

# WRONG
log "Attempting to decrypt with key prefix: ${KEY:0:4}..."

# RIGHT
log "Decrypt attempt: kid=$(hash_id $KEY_NAME) result=$result"

Truncated keys are still useful to attackers (rainbow table search space reduction; structural fingerprint).

---

Section 8: Worked examples

Review M1 — shred on flash storage

Original: scripts use shred -u to delete secret-bearing files on the USB drive.

What this skill flags:

• Section 2: shred on flash is worse than nothing
• Section 2 anti-pattern: writing secrets to non-tmpfs scratch

Remediation:

• Verify /tmp is tmpfs at script start; refuse if not
• Move all scratch to tmpfs; don't write secret-bearing files to USB at all
• Document that the USB only holds encrypted-at-rest data, never plaintext

Review M2 — set -e not specified

Original: scripts use set -uo pipefail but not -e.

What this skill flags:

• Section 3: missing -e allows silent partial-state errors

Remediation:

• Add set -euo pipefail to all secret-bearing scripts
• Add trap cleanup ERR EXIT INT TERM

Review M3 — SECRETS_ENV aggregation

Original: all credentials concatenated into one SECRETS_ENV variable.

What this skill flags:

• Section 1 anti-pattern: aggregation = single leak vector

Remediation:

• One fd per secret, OR one named pipe per secret in tmpfs with mode 600
• Never export secret-bearing variables; keep them function-local

Review L2 — YubiKey serials in .meta.json

What this skill flags:

• Section 5 anti-pattern: identifier in metadata

Remediation:

• Hash with per-USB salt; store (salt, hash) not raw serial

Review M5 — no LUKS header backup

What this skill flags:

• Section 6 missing required pattern

Remediation:

• cryptsetup luksHeaderBackup, encrypt to HQ pubkey, store off-device, document recovery procedure, test it

---

Section 9: Output format

When invoked as part of a review, produce findings in standard format. When the system is mature, produce a secret-handling-policy.md document covering Sections 1–7 with project-specific decisions.

---

Related

• At-rest companion: addons/security/secure-token-load.md (token files, modes, heredoc patterns)
• Companion skill: degraded-mode-design (cleanup hygiene fires from degraded-mode triggers)
• Companion skill: physical-threat-modeling (cold-boot, DMA attacks against in-memory secrets)

Standards referenced

• OWASP Cryptographic Storage Cheat Sheet
• OWASP Secure Headers Project
• NIST SP 800-88 — Media Sanitization (for the "shred is not enough" case)
• libsodium memory-handling documentation
• man 7 random — RNG and memory hygiene
• LUKS On-Disk Format Specification