Code Clone Assistant

Detect code clones and guide refactoring using PMD CPD (exact duplicates) + Semgrep (patterns).

Self-Evolving Skill: This skill improves through use. If instructions are wrong, parameters drifted, or a workaround was needed — fix this file immediately, don't defer. Only update for real, reproducible issues.

Tools

• PMD CPD v7.17.0+: Exact duplicate detection
• Semgrep v1.140.0+: Pattern-based detection

Tested: October 2025 - 30 violations detected across 3 sample files Coverage: ~3x more violations than using either tool alone

When to Use This Skill

Use this skill when:

• Finding duplicate code in a codebase
• Detecting DRY violations
• Refactoring similar code patterns
• Identifying copy-paste code

Why Two Tools?

PMD CPD and Semgrep detect different clone types:

Result: Using both finds ~3x more DRY violations.

Clone Types

Quick Start Workflow

# Step 1: Detect exact duplicates (PMD CPD)
pmd cpd -d . -l python --minimum-tokens 20 -f markdown > pmd-results.md

# Step 2: Detect pattern violations (Semgrep)
semgrep --config=clone-rules.yaml --sarif --quiet > semgrep-results.sarif

# Step 3: Analyze combined results (Claude Code)
# Parse both outputs, prioritize by severity

# Step 4: Refactor (Claude Code with user approval)
# Extract shared functions, consolidate patterns, verify tests

Accepted Exceptions (Known Intentional Duplication)

Not all code duplication is a problem. Some codebases deliberately use copy-and-adapt patterns where refactoring would be harmful. When running clone detection, always check for accepted exceptions before recommending refactoring.

When Duplication Is Acceptable

How to Report Accepted Exceptions

When clone detection finds duplication that matches an accepted exception pattern:

1. Report it — always show the user what was found (lines, tokens, files)
2. Flag as accepted — explicitly state it matches a known exception pattern
3. Explain why — cite the specific reason refactoring is not recommended
4. Do NOT recommend refactoring — this is the key difference from actionable findings

Example output format:

Code Clone Analysis Results

PMD CPD Findings:
  Clone 1: 115 lines (575 tokens) — base_bars → signals CTEs
    gen610_template.sql:33 ↔ gen710_template.sql:38
    Status: ACCEPTED EXCEPTION (generation-per-directory experiment)
    Reason: Each generation is immutable. Shared CTEs would break
            experiment provenance and reproducibility.

  Clone 2: 36 lines (478 tokens) — metrics aggregation
    gen610_template.sql:207 ↔ gen710_template.sql:244
    Status: ACCEPTED EXCEPTION (SQL template without include mechanism)

Actionable Findings: 0
Accepted Exceptions: 2

Project-Level Exception Configuration

Projects can declare accepted exception patterns in their CLAUDE.md:

## Code Clone Exceptions

- `sql/gen*_template.sql` — generation-per-directory experiments (immutable)
- `scripts/gen*/` — copy-and-adapt sweep scripts (no shared infrastructure)
- `tests/fixtures/` — intentional duplication for test isolation

When this section exists in a project's CLAUDE.md, the code-clone-assistant should check it before classifying findings.

Reference Documentation

For detailed information, see:

• Detection Commands - PMD CPD and Semgrep command details
• Complete Workflow - Detection, analysis, and presentation phases
• Refactoring Strategies - Approaches for addressing violations

Troubleshooting

Post-Execution Reflection

After this skill completes, check before closing:

1. Did the command succeed? — If not, fix the instruction or error table that caused the failure.
2. Did parameters or output change? — If the underlying tool's interface drifted, update Usage examples and Parameters table to match.
3. Was a workaround needed? — If you had to improvise (different flags, extra steps), update this SKILL.md so the next invocation doesn't need the same workaround.

Only update if the issue is real and reproducible — not speculative.