codeql

Files (16)

• SKILL.md
• build-fixes.md · references/
• diagnostic-query-templates.md · references/
• extension-yaml-format.md · references/
• important-only-suite.md · references/
• language-details.md · references/
• macos-arm64e-workaround.md · references/
• performance-tuning.md · references/
• quality-assessment.md · references/
• ruleset-catalog.md · references/
• run-all-suite.md · references/
• sarif-processing.md · references/
• threat-models.md · references/
• build-database.md · workflows/
• create-data-extensions.md · workflows/
• run-analysis.md · workflows/

SKILL.md (first lines)

# CodeQL Analysis

Supported languages: Python, JavaScript/TypeScript, Go, Java/Kotlin, C/C++, C#, Ruby, Swift.

**Skill resources:** Reference files and templates are located at `{baseDir}/references/` and `{baseDir}/workflows/`.

## Essential Principles

1. **Database quality is non-negotiable.** A database that builds is not automatically good. Always run quality assessment (file counts, baseline LoC, extractor errors) and compare against expected source files. A cached build produces zero useful extraction.

2. **Data extensions catch what CodeQL misses.** Even projects using standard frameworks (Django, Spring, Express) have custom wrappers around database calls, request parsing, or shell execution. Skipping the create-data-extensions workflow means missing vulnerabilities in project-specific code paths.

3. **Explicit suite references prevent silent query dropping.** Never pass pack names directly to `codeql database analyze` — each pack's `defaultSuiteFile` applies hidden filters that can produce zero results. Always generate a custom `.qls` suite file.

4. **Zero findings needs investigation, not celebration.** Zero results can indicate poor database quality, missing models, wrong query packs, or silent suite filtering. Investigate before reporting clean.

5. **macOS Apple Silicon requires workarounds for compiled languages.** Exit code 137 is `arm64e`/`arm64` mismatch, not a build failure. Try Homebrew arm64 tools or Rosetta before falling back to `build-mode=none`.

6. **Follow workflows step by step.** Once a workflow is selected, execute it step by step without skipping phases. Each phase gates the next — skipping quality assessment or data extensions leads to incomplete analysis.

## Output Directory

All generated files (database, build logs, diagnostics, extensions, results) are stored in a single output directory.

- **If the user specifies an output directory** in their prompt, use it as `OUTPUT_DIR`.
- **If not specified**, default to `./static_analysis_codeql_1`. If that already exists, increment to `_2`, `_3`, etc.

In both cases, **always create the directory** with `mkdir -p` before writing any files.

```bash
# Resolve output directory
if [ -n "$USER_SPECIFIED_DIR" ]; then
  OUTPUT_DIR="$USER_SPECIFIED_DIR"
else
  BASE="static_analysis_codeql"
  N=1
  while [ -e "${BASE}_${N}" ]; do
    N=$((N + 1))
  done
  OUTPUT_DIR="${BASE}_${N}"
fi
mkdir -p "$OUTPUT_DIR"
```

The output directory is resolved **once** at the start before any workflow executes. All workflows receive `$OUTPUT_DIR` and store their artifacts there:

```
$OUTPUT_DIR/
├── rulesets.txt                 # Selected query packs (logged after Step 3)
├── codeql.db/                   # CodeQL database (dir containing codeql-database.yml)
├── build.log                    # Build log
├── codeql-config.yml            # Exclusion config (interpreted languages)
├── diagnostics/                 # Diagnostic queries and CSVs
├── extensions/                  # Data extension YAMLs
├── raw/                         # Unfiltered analysis output
│   ├── results.sarif
│   └── <mode>.qls
└── results/                     # Final results (filtered for important-only, copied for run-all)
    └── results.sarif
```

### Database Discovery

A CodeQL database is identified by the presence of a `codeql-database.yml` marker file inside its directory. When searching for existing databases, **always collect all matches** — there may be multiple databases from previous runs or for different languages.

**Discovery command:**

```bash
# Find ALL CodeQL databases (top-level and one subdirectory deep)
find . -maxdepth 3 -name "codeql-database.yml" -not -path "*/\.*" 2>/dev/null \
  | while read -r yml; do dirname "$yml"; done
```

- **Inside `$OUTPUT_DIR`:** `find "$OUTPUT_DIR" -maxdepth 2 -name "codeql-database.yml"`
- **Project-wide (for auto-detection):** `find . -maxdepth 3 -name "codeql-database.yml"` — covers databases at the project top level (`./db-name/`) and one subdirectory deep (`./subdir/db-name/`). Does not search deeper.

Never assume a database is named `codeql.db` — discover it by its marker file.

**When multiple databases are found:**

For each discovered database, collect metadata to help the user choose:

```bash
# For each database, extract language and creation time
for db in $FOUND_DBS; do
  CODEQL_LANG=$(codeql resolve database --format=json -- "$db" 2>/dev/null | jq -r '.languages[0]')
  CREATED=$(grep '^creationMetadata:' -A5 "$db/codeql-database.yml" 2>/dev/null | grep 'creationTime' | awk '{print $2}')
  echo "$db — language: $CODEQL_LANG, created: $CREATED"
done
```

Then use `AskUserQuestion` to let the user select which database to use, or to build a new one. **Skip `AskUserQuestion` if the user explicitly stated which database to use or to build a new one in their prompt.**

## Quick Start

For the common case ("scan this codebase for vulnerabilities"):

```bash
# 1. Verify CodeQL is installed
if ! command -v codeql >/dev/null 2>&1; then
  echo "NOT INSTALLED: codeql binary not found on PATH"
else
  codeql --version || echo "ERROR: codeql found but --version failed (check installation)"
fi

# 2. Resolve output directory
BASE="static_analysis_codeql"; N=1
while [ -e "${BASE}_${N}" ]; do N=$((N + 1)); done
OUTPUT_DIR="${BASE}_${N}"; mkdir -p "$OUTPUT_DIR"
```

Then execute the full pipeline: **build database → create data extensions → run analysis** using the workflows below.

## When to Use

- Scanning a codebase for security vulnerabilities with deep data flow analysis
- Building a CodeQL database from source code (with build capability for compiled languages)
- Finding complex vulnerabilities that require interprocedural taint tracking or AST/CFG analysis
- Performing comprehensive security audits with multiple query packs

From idchain-world/id-agents, MIT.

More from idchain-world/id-agents