patch

name	patch
description	Generate candidate fixes for verified security findings. Consumes TRIAGE.json (preferred), VULN-FINDINGS.json, or a vuln-pipeline results directory. Pipeline input is delegated to the execution-verified `vuln-pipeline patch` ladder; static-analysis input gets a per-finding patch subagent + independent reviewer and is written as inert diffs for human review. Writes PATCHES/bug_NN/{patch.diff,patch_result.json}, PATCHES.md, and PATCHES.json. Use when asked to "fix the findings", "patch these vulns", "generate fixes", or "close the loop on triage".
argument-hint	<findings-path> [--repo PATH] [--top N] [--id fNNN] [--model M] [--fresh]
allowed-tools	["Read","Glob","Grep","Write","Task","Bash(python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py:*)","Bash(vuln-pipeline patch:*)","Bash(rg:*)","Bash(grep:*)","Bash(ls:*)","Bash(wc:*)","Bash(head:*)","Bash(file:*)","Bash(jq:*)"]

patch

Third leg of the static pipeline (/vuln-scan → /triage → /patch). Turns a ranked list of verified findings into candidate diffs.

The skill never applies a diff to the target repo. Output is inert text in ./PATCHES/ for a human to review and apply out-of-band — see docs/patching.md#reviewing-generated-patches. There is no --apply or --approve flag by design: the capability isn't present, so it can't be prompt-injected into use.

Invoke with /patch <findings-path> [--repo PATH] [--top N] [--id fNNN] [--model M] [--fresh].

Arguments (parse from $ARGUMENTS):

• findings path (first positional, required): TRIAGE.json, VULN-FINDINGS.json, a pipeline results/<target>/<ts>/ directory, or any JSON the /triage ingest table recognizes.
• --repo PATH: target codebase, read-only (default cwd). Required for static mode; the skill stops if cited files don't resolve under it.
• --top N: patch only the N highest-severity true positives (static mode).
• --id fNNN: patch only the finding with this id.
• --model M: passed through to vuln-pipeline patch in execution-verified mode. Ignored in static mode (subagents inherit the orchestrator's model).
• --fresh: ignore ./.patch-state/ checkpoint and start over.

Tools. Prefer Read, Glob, Grep, Write, Task. Some sessions do not provision Glob or Grep; allowed-tools is a permission filter, not a loader. When they are unavailable, fall back to the read-only Bash commands whitelisted above: rg/grep for search, ls for enumeration, head/file/wc for sniffing, jq for JSON ingest. Bash is otherwise permitted only for python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py (state I/O) and vuln-pipeline patch (execution-verified delegate). find is NOT permitted.

Write scope. The Write tool may target ONLY paths under ./PATCHES/ and ./.patch-state/. Never write into --repo, never git apply, never patch, never edit target source. If a step seems to require it, the step is wrong.

---

Checkpointing (runs before Phase 0 and after every phase)

State persists to ./.patch-state/ so a fresh /patch session resumes without re-spawning patch or reviewer subagents. All checkpoint I/O goes through python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py (atomic, JSON-validated). The Write→--from pattern keeps repo-derived bytes out of Bash argv; never pass payload via heredoc or stdin.

State files: progress.json (single source of truth: {"status": "running"|"complete", "phase_done": N, "shards_done": [...]}), phaseN.json, _chunk.tmp.

Start of run. Bash: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py load ./.patch-state

• status == "absent" OR "complete", OR --fresh in $ARGUMENTS → fresh start. Bash: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py reset ./.patch-state, proceed to Phase 0.
• status == "running" with phase_done == N → resume. Read phase0.json..phaseN.json in order (and any shard_*.json listed in shards_done), merge into working state, print Resuming from checkpoint: Phase N complete, skip to Phase N+1. Do not re-spawn any subagent whose output is already checkpointed.

End of every phase N. Write tool → ./.patch-state/_chunk.tmp with the phase's JSON, then Bash: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py save ./.patch-state <N> <name> --from ./.patch-state/_chunk.tmp

End of run. After writing PATCHES.md and PATCHES.json, Bash: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py done ./.patch-state 4

---

Phase 0: Parse arguments and detect mode

0a. Parse $ARGUMENTS

Extract findings path (first positional), --repo (default .), --top, --id, --model, --fresh. If no findings path, stop and ask.

0b. Detect mode

Inspect the findings path:

• execution-verified mode when the path is a directory containing reports/manifest.jsonl OR found_bugs.jsonl OR run_*/result.json (pipeline output). The findings have PoC bytes + ASAN traces + reproduction commands; the pipeline's verification ladder applies.
• static mode otherwise: TRIAGE.json, VULN-FINDINGS.json, generic finding JSON, or markdown. No PoC; the oracle is a fresh-context reviewer.

Record mode in working state. The two modes share Phase 1 ingest then fork at Phase 2.

Checkpoint: Write tool → ./.patch-state/_chunk.tmp: {"phase": 0, "mode": "exec"|"static", "args": {repo, top, id, model, findings_path}} Then Bash: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py save ./.patch-state 0 mode --from ./.patch-state/_chunk.tmp

---

Phase 1: Ingest and normalize

Same input contract as /triage Phase 1. Normalize every input format to a flat findings[] of dicts. Pull what's present; never guess what's absent.

1a. Recognized containers (priority order)

1. TRIAGE.json — read .findings[]. Filter to verdict == "true_positive". This is the canonical input: already verified, deduped, ranked, owner-tagged.
2. VULN-FINDINGS.json — read .findings[]. Unverified; print Warning: VULN-FINDINGS.json is unverified scanner output. Consider /triage first. and continue.
3. Pipeline results directory — one finding per reports/bug_NN/. Map report.json → description, crash.crash_type → category, ASAN top-frame → file/line. Record bug_id = NN for the --bug N delegate flag.
4. Generic *.json with a top-level list or a findings/results/ issues/vulnerabilities array.

1b. Field aliases (canonical ← also-accept)

Canonical	Also accept
file	path, location.file, filename
line	line_number, location.line, lineno
category	type, cwe, rule_id, crash_type
severity	severity_rating, level, priority
title	name, summary, message
description	details, report, body, evidence, rationale
recommendation	fix, remediation, mitigation
owner_hint	owner, component

Attach id (f001, f002, ... in ingest order; preserve existing ids from TRIAGE.json) and source (relative path of the file it came from).

1c. Filter and order

• If --id fNNN: keep only that finding.
• If --top N (static mode): sort by severity HIGH > MEDIUM > LOW then confidence desc, keep the first N.
• Drop findings with no file (cannot patch what cannot be located). Record them as skipped with reason "no source location".

1d. Locate the target codebase (static mode)

Resolve --repo. For the first 5 findings with a file, check the path resolves under repo (try as-given, then with common prefixes stripped). If none resolve, stop: tell the user the cited files aren't reachable and suggest a --repo value.

Checkpoint: Write tool → ./.patch-state/_chunk.tmp: {"phase": 1, "mode": ..., "findings": [...], "skipped": [...], "repo": ...} Then Bash: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py save ./.patch-state 1 ingest --from ./.patch-state/_chunk.tmp

---

Phase 2: Generate patches

Forks on mode.

2A. Execution-verified mode — delegate to the pipeline

The pipeline already implements the build → reproduce → regress → re-attack ladder with executable oracles. Do not reimplement it.

For each finding (or once for the whole directory if no --id/--top filter), Bash:

vuln-pipeline patch <findings_path> --model <--model arg> [--bug <bug_id>]

The pipeline writes <findings_path>/reports/bug_NN/{patch.diff, patch_result.json} itself. After it returns, Read each patch_result.json and copy verdict + rationale into working state. Set verified: "ladder_passed" when verdict.passed == true, else verified: "ladder_failed".

If the CLI exits non-zero (no build_command, missing target config), record the stderr as the finding's error and continue with remaining findings.

Skip Phase 3 (the ladder is the verifier). Proceed to Phase 4.

Checkpoint per finding: Write tool → ./.patch-state/_chunk.tmp = {"id": ..., "verified": ..., "verdict": ..., "diff_path": ...}, then Bash: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py shard ./.patch-state <id> --from ./.patch-state/_chunk.tmp. After all findings, write the consolidated phase payload to _chunk.tmp then: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py save ./.patch-state 2 generate --from ./.patch-state/_chunk.tmp

2B. Static mode — one patch subagent per finding

One Task per finding, all in a SINGLE assistant message for parallel execution. subagent_type: "general-purpose". Never set run_in_background — you need the diff text, not an async handle.

Each subagent has read-only access to --repo. It cannot modify the target; it emits the diff as text in its response. The orchestrator writes that text to PATCHES/bug_NN/patch.diff.

Patch subagent prompt (assemble once, reuse per finding)

You are conducting authorized security research as part of a defensive
assessment. Your task: write a candidate fix for ONE verified vulnerability
finding in a codebase you have read-only access to.

You may use Read, Glob, and Grep ONLY on paths inside {REPO_PATH}. You may
NOT build, run, install, edit files on disk, or reach the network. You will
emit the fix as a unified diff in your final response; you will NOT apply it.

────────────────────────────────────────────────────────────────────────
FINDING:

  id:        {id}
  file:      {file}
  line:      {line}
  category:  {category}
  severity:  {severity}
  title:     {title}

  description:
  {description}

  recommendation:
  {recommendation or "(none provided)"}

────────────────────────────────────────────────────────────────────────
PROCEDURE:

1. READ THE CODE. Open {file} at line {line} and the surrounding function.
   Understand what the code does — do not trust the finding's description as
   the only source.

2. ROOT CAUSE FIRST. Trace backward from the cited sink to where the bad
   value or missing check originates. The fix usually belongs there, not at
   the line the scanner flagged. Name the root-cause location (file:line).

3. VARIANT HUNT. Grep for sibling call sites with the same pattern. Your fix
   should cover all of them, or your rationale should say why not.

4. MINIMAL DIFF. Smallest change that fixes the root cause. No refactoring,
   no drive-by cleanup, no reformatting, no comment-only changes. Match the
   surrounding code's style (brace placement, naming, error handling).

5. ADVERSARIAL SELF-CHECK. Re-read your diff as an attacker. Name one input
   variation that would reach the same bad state without tripping your
   change. If you can name one, your fix is at the wrong layer — go back to
   step 2.

6. REGRESSION TEST. As part of the diff, add ONE test case that fails before
   your change and passes after — placed wherever the project keeps its
   tests (look for test_*/, *_test.*, tests/, spec/). If no test directory
   exists, omit the test and say so in <test_note>.

────────────────────────────────────────────────────────────────────────
OUTPUT — your final response MUST contain exactly these tags. Emit the diff
verbatim between the markers; do NOT wrap it in ``` fences.

<patch_diff>
--- a/path/to/file
+++ b/path/to/file
@@ ... @@
 context line
-removed line
+added line
</patch_diff>
<rationale>what changed and why, mechanically — file:line of root cause,
what the change enforces</rationale>
<variants_checked>file:function pairs you grepped for the same
pattern, and whether each needed the fix</variants_checked>
<bypass_considered>the input variation you tried in step 5 and why it
no longer reaches the bad state</bypass_considered>
<test_note>where the regression test landed, or why none was
added</test_note>

If you determine the finding is NOT fixable as described (wrong file, code
already patched, finding is a false positive), emit:

<patch_diff>NONE</patch_diff>
<rationale>why no patch is appropriate</rationale>

Spawn

For each finding in findings[], build a Task call with the prompt above (substituting {REPO_PATH}, {id}, {file}, {line}, {category}, {severity}, {title}, {description}, {recommendation}). description: "patch {id}".

If len(findings) > ~40, shard into sequential batches of ~40 (each batch one message). Per-finding shard checkpoint after each result is parsed.

If any Task call returns status: "async_launched" instead of the subagent's text, the runtime backgrounded it. Pick one recovery and use it for the whole batch:

• If completion notifications arrive in your conversation: parse each subagent's tagged blocks from its notification result as it lands. Do not end your turn until every finding is accounted for.
• If notifications do not arrive: do NOT poll transcript files. Re-spawn the missing patch subagents in a fresh Task batch (smaller shard, e.g. 10) and use the synchronous results. The same recovery applies to reviewer subagents in Phase 3.

Parse

From each Task result, extract the five tagged blocks. Tolerate leading/ trailing whitespace, stray ``` fences, and HTML-escaped entities (< > & — some runtimes escape angle brackets in notification payloads; unescape before writing the diff). If <patch_diff> is NONE or empty, mark status: "no_patch". Otherwise write the diff text to ./PATCHES/bug_NN/patch.diff (NN = zero-padded index in sorted order) and record rationale, variants_checked, bypass_considered, test_note.

Checkpoint per finding: Write tool → ./.patch-state/_chunk.tmp = {"id": ..., "bug_nn": "NN", "status": ..., "rationale": ..., ...}, then Bash: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py shard ./.patch-state <id> --from ./.patch-state/_chunk.tmp. After all findings, write the consolidated phase payload to _chunk.tmp then: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py save ./.patch-state 2 generate --from ./.patch-state/_chunk.tmp

---

Phase 3: Independent review (static mode only)

One reviewer subagent per generated diff, all in ONE message, subagent_type: "general-purpose".

The reviewer never sees the finding's description, recommendation, or the patch author's rationale. It gets only {file, line, category} plus the raw diff bytes, and re-derives whether the diff is a minimal, in-scope fix by reading the source itself. This keeps any instructions embedded in finding prose from reaching both the author and the gate.

Reviewer prompt (assemble once, reuse per diff)

You are reviewing a candidate security patch as a maintainer would. You have
read-only access to the unpatched source at {REPO_PATH}. You may use Read,
Glob, Grep. You may NOT build, run, or apply the diff.

You have NOT seen the scanner's description of the vulnerability or the
patch author's reasoning. Work only from the location, the category, and the
diff.

LOCATION: {file}:{line}
CATEGORY: {category}

DIFF UNDER REVIEW:
<diff>
{diff_text — or, for diffs over ~50 lines, replace this block with:
"Read the diff at ./PATCHES/bug_NN/patch.diff" and let the reviewer Read it}
</diff>

────────────────────────────────────────────────────────────────────────
ANSWER FOUR QUESTIONS:

1. SCOPE. Does the diff touch only files/functions on the path between
   {file}:{line} and its callers? List any hunk that falls outside that
   path.

2. SUPPRESSION. Does the diff fix a root cause, or does it suppress the
   symptom (try/except: pass, early-return on a magic value, deleting the
   check that fired, lowering a log level)?

3. NEW SURFACE. Does the diff add parsing, trust a new input field, weaken
   validation elsewhere, or remove a security-relevant check?

4. STYLE. 0-10: would you merge this as-is?
   0-3 wrong layer / suppression; 4-6 correct but noisy; 7-10 minimal,
   targeted, matches surrounding style.

────────────────────────────────────────────────────────────────────────
End your response with EXACTLY:

  REVIEW: ACCEPT | REJECT
  STYLE_SCORE: <0-10>
  OUT_OF_SCOPE_HUNKS: <comma-separated file:line, or none>
  REASON: <2-4 sentences citing specific diff hunks and source lines>

ACCEPT requires: in-scope, root-cause fix, no new attack surface,
style >= 5. Otherwise REJECT.

Spawn and parse

One Task per finding with status != "no_patch". Parse the trailing block. Attach review, style_score, out_of_scope_hunks, review_reason to the finding. Set verified: "static_review_only" for every static-mode result regardless of ACCEPT/REJECT — the label describes the verification class, not the outcome.

Checkpoint: Write tool → ./.patch-state/_chunk.tmp: {"phase": 3, "findings": [...]} Then Bash: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py save ./.patch-state 3 review --from ./.patch-state/_chunk.tmp

---

Phase 4: Output

4a. Per-finding patch_result.json

For each finding (both modes), Write ./PATCHES/bug_NN/patch_result.json:

{
  "id": "f003",
  "source": "TRIAGE.json#2",
  "title": "...",
  "file": "...",
  "line": 0,
  "category": "...",
  "severity": "HIGH",
  "owner_hint": "...",
  "mode": "exec" | "static",
  "verified": "ladder_passed" | "ladder_failed" | "static_review_only",
  "review": "ACCEPT" | "REJECT" | null,
  "style_score": 0,
  "out_of_scope_hunks": []
   
   
   
   
   
        

In exec mode, also Read the pipeline's <findings_path>/reports/bug_NN/patch.diff and Write its bytes to ./PATCHES/bug_NN/patch.diff so both modes land in the same place.

4b. ./PATCHES.json

{
  "patch_completed": true,
  "mode": "exec" | "static",
  "repo": "...",
  "summary": {
    "input_count": 0,
    "patched": 0,
    "no_patch": 0,
    "accepted": 0,
    "rejected": 0,
    "ladder_passed": 0
  },
  "findings": [ { ...patch_result.json shape... } ]
}

4c. ./PATCHES.md (incremental)

Step 1 — header. Write tool → ./PATCHES.md (clobbers prior):

# Candidate Patches

{if mode == "static":}
> **Static review only.** These diffs were authored and reviewed by
> independent agents reading source. They were NOT compiled, run, or
> re-attacked. Read each diff yourself before applying — see
> `docs/patching.md#reviewing-generated-patches` for what to look for.

{if mode == "exec":}
> **Execution-verified.** Each diff passed (or failed) the pipeline
> verification ladder: build → reproduce → regress → re-attack. The ladder
> proves the crash is gone, not that the diff introduces no new problems.

**Input:** {findings_path} · **Repo:** {repo} · {N} findings → {M} diffs

---

Step 2 — per finding (sorted: ACCEPT/ladder_passed first, then by severity). Write ./.patch-state/_chunk.tmp:

## bug_{NN}: [{severity}] {title}  ({id})

`{file}:{line}` · {category} · owner: {owner_hint or "?"}
**Status:** {verified} · review {review or "n/a"} · style {style_score or "n/a"}/10
**Diff:** `PATCHES/bug_{NN}/patch.diff` ({hunk count} hunks, {line count} lines)

**Rationale:** {rationale}
**Variants checked:** {variants_checked}
**Bypass considered:** {bypass_considered}
{if review == "REJECT":}
> **Rejected by reviewer:** {review_reason}
{if out_of_scope_hunks:}
> **Out-of-scope hunks:** {out_of_scope_hunks}

---

Then checkpoint.py append ./PATCHES.md --from ./.patch-state/_chunk.tmp.

Step 3 — footer. Append a ## Skipped table for findings with no file or status == "no_patch", one line each with the reason.

Checkpoint (final): Bash: python3 ~/.hermes/skills/community/defending-code-reference-harness/_lib/checkpoint.py done ./.patch-state 4

4d. Terminal summary

Under ~10 lines:

Patches generated ({mode} mode): {N} findings → {M} diffs.

  Accepted:  {n}   {title of top accepted}
  Rejected:  {n}
  No patch:  {n}
  {if exec:} Ladder passed: {n}/{M}

Wrote ./PATCHES/bug_NN/, ./PATCHES.md, ./PATCHES.json
{if static:} These are drafts. Review before applying — see docs/patching.md.

---

Guard rails

• The skill never applies diffs. No git apply, no patch, no Edit against --repo. If you find yourself needing to, the design is wrong.
• Write only under ./PATCHES/ and ./.patch-state/.
• Reviewer isolation. The reviewer prompt receives {file, line, category, diff} and nothing else from the finding. Do not pass it description, recommendation, exploit_scenario, or the patch author's rationale.
• Always set subagent_type. Forking would leak every finding's prose into every patch subagent.
• All Task calls for a phase in ONE message. Serial spawning is correct but N× slower.
• Checkpoint before starting the next phase, every time.
• Exec mode delegates, never reimplements. If vuln-pipeline patch isn't on PATH, stop and tell the user; don't fall back to static mode silently.

---

Testing this skill

Static mode against the canary fixture:

/vuln-scan targets/canary
/triage VULN-FINDINGS.json --repo targets/canary --auto
/patch TRIAGE.json --repo targets/canary --top 3

Expected: three diffs under PATCHES/bug_00..02/, each verified: "static_review_only", review: ACCEPT, style ≥ 7 for the planted overflow/UAF/format-string bugs.

Execution-verified mode against pipeline output:

vuln-pipeline run drlibs --runs 3 --parallel --stream --model <m>
/patch results/drlibs/<ts>/ --model <m>

Expected: delegates to vuln-pipeline patch, surfaces verified: "ladder_passed" per bug, copies diffs into ./PATCHES/.

---

Design notes

• TRIAGE.json is canonical input because patching unverified findings wastes tokens on false positives. VULN-FINDINGS.json is accepted with a warning for convenience.
• Static mode emits a regression test inside the diff rather than running it. The skill cannot execute target code (constraint of the static pipeline); the test is for the human who applies the diff.
• Reviewer never sees finding prose. Target source can contain injected instructions that survive into a scanner's description field. The patch author sees that prose (it has to, to know what to fix); the reviewer doesn't, so injected text cannot pass its own gate.
• verified is the verification class, not pass/fail. static_review_only means "an agent read it" regardless of ACCEPT/REJECT. ladder_passed/ladder_failed means "ASAN decided." Downstream tooling should branch on this field, not on review.
• Output shape matches the pipeline (PATCHES/bug_NN/{patch.diff, patch_result.json}) so consumers don't care which mode produced it.