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

/beagle-core: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”).

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.
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).
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).
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.
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 /beagle-core:review-llm-artifacts first."

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 /beagle-core:verify-llm-artifacts 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 /beagle-core:review-llm-artifacts 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, spawn parallel agents per category with Task tool:

Task: Apply safe fixes for category "{category}"
Files: [list of files with findings in this category]
Instructions: Apply each fix, preserving surrounding code. Report success/failure per fix.

Categories to parallelize:

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
/beagle-core:fix-llm-artifacts --dry-run

# Fix only dead code issues
/beagle-core:fix-llm-artifacts --category dead-code

# Full codebase scan and fix
/beagle-core:fix-llm-artifacts --all

# Fix style issues only, preview first
/beagle-core:fix-llm-artifacts --category style --dry-run