xgrep-fix

name	xgrep-fix
description	Fixes a whole set of xgrep findings — or just the triage-confirmed true positives in a findings.json — in one pass via the verify/apply harness. Auto-applies deterministic fixes (xgrep fix --confirmed), drives the assisted author/verify/apply loop per finding, and surfaces advisory guidance, reporting a per-fingerprint summary. Use to remediate many findings at once after a scan or triage.
allowed-tools	Bash Read Glob Grep

xgrep Fix (batch)

Remediate a set of findings and prove each fix holds with xgrep's verify/apply harness. This is the batch layer over xgrep-remediate: it takes the outcome of a scan or a triage run, partitions the findings by fix tier, and drives each tier to a verified result. xgrep owns the mechanical gates (parse-clean, re-scan, atomic write); you own the reasoning that authors any non-mechanical edit.

When to Use

• Fixing many findings from a scan in one pass (not one finding at a time)
• Fixing exactly the triage-confirmed true positives in a findings.json (the verdicts xgrep-triage wrote into extra.triage)
• Running a deterministic-fix sweep across a codebase with a verified summary

When NOT to Use

• Deciding whether findings are real — that is triage. Use xgrep-triage first; with --confirmed this skill trusts the extra.triage true-positive verdicts.
• Fixing a single, already-known finding — use xgrep-remediate (simpler).
• Suppressing/ignoring findings, or creating rules (xgrep-rule-creator).

Rules are built in. Every command below uses xgrep's bundled rules by default (600+ across 14 languages, security + secrets) — no -f needed. Pass -f <rules-path> only when the findings came from a custom rule pack; then add the same -f to every scan / fix verify / fix apply so the re-scan gate uses the rule that produced the finding.

Step 1 — Resolve the input (one artifact: findings.json)

The input is a scan findings.json ({results:[...]}). It is the single source of truth: each finding carries its tier and contract (extra.fix_info — how to fix), its fingerprint, and — if it has been triaged — a verdict (extra.triage — whether to fix). There is no separate markdown report to parse.

Two cases, distinguished by whether the findings carry extra.triage:

• Triaged input (preferred) — findings reviewed by xgrep-triage (or a human) carry extra.triage.status (true-positive / false-positive / needs-review). Fix only the confirmed true-positives with --confirmed; false-positive findings are skipped automatically. If the file isn't triaged yet, run /xgrep-triage first (it writes extra.triage back into findings.json).

• Un-triaged input — a raw scan with no verdicts. Fix every finding, narrowed by scope (severity / confidence / rule) rather than by review. (Even here, any finding already marked false-positive is never fixed.)

If you don't have a findings.json yet:

xgrep scan --json <target> > findings.json

Step 2 — Partition by tier and present the plan

Bucket the selected findings by extra.fix_info.kind:

• deterministic — xgrep already computed the exact edit (Step 3).
• assisted — xgrep emits a fix contract; you author the edit (Step 4).
• advisory — guidance only, no code edit (Step 5).

Show the plan before mutating anything: counts per tier × severity, and the work order (ERROR → WARNING → INFO; within a severity, injection/auth before config). Get a clean picture of scope first — a batch that silently skips half the findings is worse than one that says what it will and won't touch.

Step 3 — Deterministic: auto-apply in one batch

Pipe the whole findings.json through the harness — no need to pre-filter. With triaged input, --confirmed keeps only true-positive findings (and always skips false-positive); everything else falls to out-of-scope, reported not dropped:

# Triaged input: fix only the confirmed true-positives, verified + atomic.
xgrep fix apply --confirmed < findings.json

# Preview first (no writes) — same verdict fix apply will return.
xgrep fix verify --confirmed < findings.json

For un-triaged input, drop --confirmed and scope with --rule / --max-severity / --min-confidence as needed. fix only ever auto-applies the deterministic tier from a piped report — assisted findings come back as needs-agent and advisory as advisory — so piping the whole file and letting fix apply just the mechanical ones is safe. Add --strict to exit non-zero on any rejection (use in CI). The re-scan gate runs by default. Collect the streamed FixOutcomes (keyed by fingerprint) for the report.

Step 4 — Assisted: drive the loop per finding

--confirmed only governs the deterministic auto-apply batch (Step 3); for assisted findings, you apply the same filter — with triaged input, author edits only for findings whose extra.triage.status == "true-positive", and skip false-positive / needs-review.

For each such assisted finding, run the per-finding remediation loop — the same one xgrep-remediate documents:

1. Read extra.fix_info.contract: unsafe_region (byte/line span + enclosing function), strategy (the fix approach), acceptance_criteria (what xgrep will verify). The evidence (dataflow_trace, context) rides on the same finding.

2. Read the file around unsafe_region; if you need types or flow, investigate with the code graph (xgrep graph context <fn> --depth 2, xgrep graph paths <src> <sink>).

3. Author byte-span replacements and verify (never writes):

   echo '{"path":"src/db.py","rule_id":"py-sql-injection","edits":[
     {"start_byte":420,"end_byte":480,"replacement":"cur.execute(\"… WHERE id=%s\", (uid,))"}]}' \
     | xgrep fix verify
   

4. If accepted is false, adjust per reason and re-verify:

   reason	Next move
   span-conflict	Re-read the file and recompute byte offsets (they shift after any prior apply); make spans disjoint.
   parse-error	Fix the syntax of replacement; verify the snippet parses in isolation.
   finding-not-cleared	The vulnerable pattern still matches — actually remove it (e.g. parameterize, don't reformat).
   new-finding-introduced	Inspect the new finding in the diff; pick a fix that doesn't trade one bug for another.
   no-change	Re-derive the span; ensure replacement differs from the spanned bytes.

5. Apply once accepted (fix apply writes the accepted edit atomically):

   echo '{…candidate…}' | xgrep fix apply
   

Re-read offsets after every apply — byte offsets are absolute, so every later offset in a file shifts once a write lands. Fix one finding fully (verify → apply → confirm) before moving to the next in the same file, or author all edits for a file against a single fresh scan. To author several candidates across files at once, stream them as NDJSON: xgrep fix apply --batch (one FixOutcome per line).

For the full rejection-reason playbook and the fix-contract schema, see the xgrep-remediate skill.

Step 5 — Advisory: surface, don't auto-edit

For advisory findings, read extra.fix_info.hint and present it as a hand-fix action item (e.g. rotate the leaked secret and purge it from history — a code edit won't fix it). Never mark an advisory finding as fixed automatically.

Step 6 — Report

Emit a consolidated summary keyed by fingerprint, mirroring FixReport.summary:

• Per tier: how many applied / verified / rejected / advisory / out-of-scope / stale-cache.
• For anything not cleared, the rejection reason and a short next step.
• A residual worklist: assisted findings you could not author a passing edit for, and every advisory item, so nothing is silently dropped.

Never report a finding fixed without a clean re-scan — the harness enforces this, and your summary should reflect only harness-confirmed outcomes.

Over MCP

The same operations are available as fix_verify (read-only) and fix_apply (writes the accepted edit). Both run the identical harness, so a rejected candidate is never written; iterate with fix_verify, commit with fix_apply.

References

• Batch workflow, input modes & triage→findings join: batch-workflow.md
• Outcome schema, fingerprint join & NDJSON streaming: outcome-reference.md

Tips

• Plan before you mutate. Show the tier × severity breakdown first; a batch that hides what it skipped is worse than one that names it.
• Deterministic is free — sweep it first. One fix apply < selected.json clears the whole mechanical tier; spend your reasoning on the assisted tier.
• Tight edits win. The smallest span that satisfies the acceptance_criteria is least likely to hit span-conflict or new-finding-introduced.
• Gate in CI. xgrep fix apply --strict < selected.json exits non-zero if any fix is rejected, so a pipeline fails loudly instead of skipping silently.