Fix LLM Artifacts

Apply fixes from a previous review-llm-artifacts run with automatic safe/risky classification. If .beagle/llm-artifacts-verification.json exists, skip findings marked false_positive and treat inconclusive like risky fixes (prompt or skip per user).

Usage

Invoke the fix-llm-artifacts skill, optionally passing these flags:

fix-llm-artifacts [--dry-run] [--all] [--category <name>]

Flags:

• --dry-run - Show what would be fixed without changing files
• --all - Fix entire codebase (runs review-llm-artifacts --all first if no review JSON)
• --category <name> - Only fix specific category: tests|dead-code|abstraction|style

Instructions

Hard gates

Sequence matters. Do not apply fixes until each pass condition is satisfied (these steps are not “internal verification”).

1. Working tree — git status --porcelain is empty or a stash was created with message beagle-core: pre-fix-llm-artifacts backup and git stash list shows it. If the user refuses stash/backup, stop or document explicit acceptance of risk in the report before edits.
2. Review artifact on disk — .beagle/llm-artifacts-review.json exists, or --all completed a review-llm-artifacts run that wrote that file. Otherwise stop (no fixes from memory or guesses). 2a. Echo + ID lock (anti-confabulation) — After loading the review (Section 3), echo the finding table (id | category | file:line | description) from the parsed JSON and record the exact id set as the locked id set. You fix only findings in this set; never fix a finding inferred from the branch name, directory, or memory. Every fix you apply or skip maps 1:1 to a locked id. See the review-verification-protocol skill → Anti-confabulation (gate 0). 2b. Per-fix existence precondition — Before editing for any finding, confirm (i) its id is in the locked set, and (ii) the cited file exists and the cited code is actually present at file:line (read it now). If the file or code is absent, do not edit — the finding is stale or confabulated; mark it skipped with a reason and move on. Never create or rewrite a file to match a finding.
3. Stale review — If jq -r '.git_head' .beagle/llm-artifacts-review.json ≠ git rev-parse HEAD, prompt to re-run review. y → re-run review, then continue. n → abort the fix pass (do not apply fixes against stale findings).
4. Verification overlay — If .beagle/llm-artifacts-verification.json exists, it must parse; build exclude/inconclusive sets before partitioning (Section 4). On parse failure, stop and report the error.
5. Risky fixes — No code_removal, logic_change, mock_boundary, abstraction_change, or test_refactor work without the interactive choice in Section 6 (or s to skip all remaining risky items).

Post-edit: Sections 7–8 pass only when invoked tools exit successfully (non-zero = failure; keep JSON artifacts per Cleanup).

1. Parse Arguments

Extract flags from $ARGUMENTS:

• --dry-run - Preview mode only
• --all - Full codebase scan
• --category <name> - Filter to specific category

2. Pre-flight Safety Checks

# Check for uncommitted changes
git status --porcelain

If working directory is dirty, warn:

Warning: You have uncommitted changes. Creating a git stash before proceeding.
Run `git stash pop` to restore if needed.

Create stash if dirty:

git stash push -m "beagle-core: pre-fix-llm-artifacts backup"

3. Load Review Results

Check for existing review file:

cat .beagle/llm-artifacts-review.json 2>/dev/null

If file missing:

• If --all flag: Run review-llm-artifacts --all first to produce a full-project review
• Otherwise: Fail with: "No review results found. Run the review-llm-artifacts skill first."

Echo + lock ids (gate 2a): Once the file is present, print every finding from the parsed JSON and lock the id set before partitioning:

python3 - <<'PY'
import json
r = json.load(open('.beagle/llm-artifacts-review.json'))
f = r['findings']
if not isinstance(f, list) or not f:
    raise SystemExit("No findings to lock; aborting.")
ids = [x.get('id') for x in f]
if any(not isinstance(i, int) for i in ids):
    raise SystemExit("All finding ids must be integers; aborting.")
if len(set(ids)) != len(ids):
    raise SystemExit("Duplicate finding ids detected; aborting.")
print("| id | category | file:line | description |")
print("|----|----------|-----------|-------------|")
for x in f:
    desc = (x.get('description') or '').replace('|', '\\|')[:80]
    print(f"| {x['id']} | {x.get('category')} | {x.get('file')}:{x.get('line')} | {desc} |")
print("Locked ids: {" + ", ".join(str(i) for i in sorted(set(ids))) + "}")
PY

Adjudicate and fix only the ids above. If your sense of what to fix differs from this table, the table wins.

Optional verification overlay — if .beagle/llm-artifacts-verification.json exists:

• Build a set of finding ids with status: false_positive → exclude these from all fix lists.
• Finding ids with status: inconclusive → always follow risky-fix handling (Section 6), even if fix_safety was Safe in the review.
• Finding ids with status: confirmed_issue → use review JSON fix_safety / risk as usual.

If verification is missing, warn when applying deletes or dead-code fixes: "For fewer false positives, run the verify-llm-artifacts skill first."

If file exists, validate freshness:

# Get stored git HEAD, scope, and target from JSON
stored_head=$(jq -r '.git_head'   .beagle/llm-artifacts-review.json)
stored_scope=$(jq -r '.scope // "all"'  .beagle/llm-artifacts-review.json)
stored_target=$(jq -r '.target // "."'  .beagle/llm-artifacts-review.json)
current_head=$(git rev-parse HEAD)

if [ "$stored_head" != "$current_head" ]; then
  echo "Warning: Review was run at commit $stored_head, but HEAD is now $current_head"
fi

If stale, prompt: "Review results are stale. Re-run review? (y/n)".

• y → re-run review-llm-artifacts with the original scope and target read from the stale JSON, then reload. This preserves the user's original intent; do not silently widen or narrow the scope, which would apply fixes unrelated to the user's diff (or miss files they cared about). Concretely:
  • scope == "changed" → invoke review-llm-artifacts "$stored_target" (default scope is already changed-files).
  • scope == "all" → invoke review-llm-artifacts --all "$stored_target".
  • If scope or target is missing from the JSON (pre-schema review), do not abort. Assume scope = "all" and target = ".", then warn:

    "Review JSON predates the scope/target schema; re-running as a full-project scan (--all). If you meant a narrower scope (the default changed-files diff, or a subdirectory), cancel now and re-run the review-llm-artifacts skill explicitly." Proceed only if the user does not cancel.

• n → abort (do not apply fixes; stale findings are not trustworthy).

4. Partition Findings by Safety

Parse findings from JSON and classify by fix_safety field (after applying verification overlay from step 3):

Safe Fixes (auto-apply):

• unused_import - Unused imports
• todo_comment - Stale TODO/FIXME comments
• dead_code_obvious - Obviously unreachable code
• verbose_comment - Overly verbose LLM-style comments
• redundant_type - Redundant type annotations

Risky Fixes (require confirmation):

• test_refactor - Test structure changes
• abstraction_change - Class/function extraction
• code_removal - Removing functional code
• mock_boundary - Test mock scope changes
• logic_change - Any behavioral modifications

5. Apply Safe Fixes

If --dry-run:

## Safe Fixes (would apply automatically)

| File | Line | Type | Description |
|------|------|------|-------------|
| src/api.py | 15 | unused_import | Remove `from typing import List` |
| src/models.py | 42 | verbose_comment | Remove 23-line docstring |
...

Otherwise, apply the safe fixes per category. If the agent supports subagents, dispatch one per category in parallel; otherwise work through the categories sequentially yourself, applying the identical per-finding contract below and producing the same per-fix report.

Apply safe fixes for category "{category}"
Files: [list of files with findings in this category]
Instructions: For EACH finding, first confirm it is in the locked id set and that the
cited code exists at file:line (read it). If the file or code is absent, skip the finding
with a reason — do NOT create or rewrite a file to match the finding. Then apply each
confirmed fix, preserving surrounding code. Report success/failure/skip per fix by id.

Categories (parallelized across subagents when supported, otherwise handled sequentially):

• style - Comments, formatting
• dead-code - Imports, unreachable code
• tests - Test-related safe fixes
• abstraction - Safe refactors

6. Handle Risky Fixes

For each risky fix, prompt interactively:

[src/services/auth.py:156] Remove seemingly unused authenticate_legacy() method?
This method has no callers in the codebase but may be used externally.
(y)es / (n)o / (s)kip all risky:

Track user choices:

• y - Apply this fix
• n - Skip this fix
• s - Skip all remaining risky fixes

7. Post-Fix Verification

Detect project type and run appropriate linters:

Python:

# Check if ruff config exists
if [ -f "pyproject.toml" ] || [ -f "ruff.toml" ]; then
    ruff check --fix .
    ruff format .
fi

# Check if mypy config exists
if [ -f "pyproject.toml" ] || [ -f "mypy.ini" ]; then
    mypy .
fi

TypeScript/JavaScript:

# Check for eslint
if [ -f "eslint.config.js" ] || [ -f ".eslintrc.json" ]; then
    npx eslint --fix .
fi

# Check for TypeScript
if [ -f "tsconfig.json" ]; then
    npx tsc --noEmit
fi

Go:

if [ -f "go.mod" ]; then
    go vet ./...
    go build ./...
fi

8. Run Tests

# Python
if [ -f "pyproject.toml" ] || [ -f "pytest.ini" ]; then
    pytest
fi

# JavaScript/TypeScript
if [ -f "package.json" ]; then
    npm test 2>/dev/null || yarn test 2>/dev/null || true
fi

# Go
if [ -f "go.mod" ]; then
    go test ./...
fi

9. Report Results

## Fix Summary

### Applied Fixes
- [x] src/api.py:15 - Removed unused import `List`
- [x] src/models.py:42-64 - Removed verbose docstring
- [x] src/auth.py:156-189 - Removed dead method (user confirmed)

### Skipped Fixes
- [ ] src/services/cache.py:23 - User declined risky fix
- [ ] tests/test_api.py:45 - Test refactor skipped

### Verification Results
- Linter: PASSED
- Type check: PASSED
- Tests: PASSED (42 passed, 0 failed)

### Diff Summary
```bash
git diff --stat

Cleanup

On successful completion (all verifications pass):

rm -f .beagle/llm-artifacts-review.json .beagle/llm-artifacts-verification.json

If any verification fails, keep the files and report:

Review file preserved at .beagle/llm-artifacts-review.json
Fix issues and re-run, or restore with: git stash pop

Example

# Preview all fixes without applying
fix-llm-artifacts --dry-run

# Fix only dead code issues
fix-llm-artifacts --category dead-code

# Full codebase scan and fix
fix-llm-artifacts --all

# Fix style issues only, preview first
fix-llm-artifacts --category style --dry-run