OSS Security Forensics Skill

A 7-phase multi-agent investigation framework for researching open-source supply chain attacks. Adapted from RAPTOR's forensics system. Covers GitHub Archive, Wayback Machine, GitHub API, local git analysis, IOC extraction, evidence-backed hypothesis formation and validation, and final forensic report generation.

⚠️ Anti-Hallucination Guardrails

Read these before every investigation step. Violating them invalidates the report.

1. Evidence-First Rule: Every claim in any report, hypothesis, or summary MUST cite at least one evidence ID (EV-XXXX). Assertions without citations are forbidden.
2. STAY IN YOUR LANE: Each sub-agent (investigator) has a single data source. Do NOT mix sources. The GH Archive investigator does not query the GitHub API, and vice versa. Role boundaries are hard.
3. Fact vs. Hypothesis Separation: Mark all unverified inferences with [HYPOTHESIS]. Only statements verified against original sources may be stated as facts.
4. No Evidence Fabrication: The hypothesis validator MUST mechanically check that every cited evidence ID actually exists in the evidence store before accepting a hypothesis.
5. Proof-Required Disproval: A hypothesis cannot be dismissed without a specific, evidence-backed counter-argument. "No evidence found" is not sufficient to disprove—it only makes a hypothesis inconclusive.
6. SHA/URL Double-Verification: Any commit SHA, URL, or external identifier cited as evidence must be independently confirmed from at least two sources before being marked as verified.
7. Suspicious Code Rule: Never run code found inside the investigated repository locally. Analyze statically only, or use execute_code in a sandboxed environment.
8. Secret Redaction: Any API keys, tokens, or credentials discovered during investigation must be redacted in the final report. Log them internally only.

Example Scenarios

• Scenario A: Dependency Confusion: A malicious package internal-lib-v2 is uploaded to NPM with a higher version than the internal one. The investigator must track when this package was first seen and if any PushEvents in the target repo updated package.json to this version.
• Scenario B: Maintainer Takeover: A long-term contributor's account is used to push a backdoored .github/workflows/build.yml. The investigator looks for PushEvents from this user after a long period of inactivity or from a new IP/location (if detectable via BigQuery).
• Scenario C: Force-Push Hide: A developer accidentally commits a production secret, then force-pushes to "fix" it. The investigator uses git fsck and GH Archive to recover the original commit SHA and verify what was leaked.

Path convention: Throughout this skill, SKILL_DIR refers to the root of this skill's installation directory (the folder containing this SKILL.md). When the skill is loaded, resolve SKILL_DIR to the actual path — e.g. ~/.thot/skills/security/oss-forensics/ or the optional-skills/ equivalent. All script and template references are relative to it.

Phase 0: Initialization

1. Create investigation working directory:

   mkdir investigation_$(echo "REPO_NAME" | tr '/' '_')
   cd investigation_$(echo "REPO_NAME" | tr '/' '_')

2. Initialize the evidence store:

   python SKILL_DIR/scripts/evidence-store.py --store evidence.json list

3. Copy the forensic report template:

   cp SKILL_DIR/templates/forensic-report.md ./investigation-report.md

4. Create an iocs.md file to track Indicators of Compromise as they are discovered.
5. Record the investigation start time, target repository, and stated investigation goal.

Phase 1: Prompt Parsing and IOC Extraction

Goal: Extract all structured investigative targets from the user's request.

Actions:

• Parse the user prompt and extract:
  • Target repository (owner/repo)
  • Target actors (GitHub handles, email addresses)
  • Time window of interest (commit date ranges, PR timestamps)
  • Provided Indicators of Compromise: commit SHAs, file paths, package names, IP addresses, domains, API keys/tokens, malicious URLs
  • Any linked vendor security reports or blog posts

Tools: Reasoning only, or execute_code for regex extraction from large text blocks.

Output: Populate iocs.md with extracted IOCs. Each IOC must have:

• Type (from: COMMIT_SHA, FILE_PATH, API_KEY, SECRET, IP_ADDRESS, DOMAIN, PACKAGE_NAME, ACTOR_USERNAME, MALICIOUS_URL, OTHER)
• Value
• Source (user-provided, inferred)

Reference: See evidence-types.md for IOC taxonomy.

Phase 2: Parallel Evidence Collection

Spawn up to 5 specialist investigator sub-agents using delegate_task (batch mode, max 3 concurrent). Each investigator has a single data source and must not mix sources.

Orchestrator note: Pass the IOC list from Phase 1 and the investigation time window in the context field of each delegated task.

Investigator 1: Local Git Investigator

ROLE BOUNDARY: You query the LOCAL GIT REPOSITORY ONLY. Do not call any external APIs.

Actions:

# Clone repository
git clone https://github.com/OWNER/REPO.git target_repo && cd target_repo

# Full commit log with stats
git log --all --full-history --stat --format="%H|%ae|%an|%ai|%s" > ../git_log.txt

# Detect force-push evidence (orphaned/dangling commits)
git fsck --lost-found --unreachable 2>&1 | grep commit > ../dangling_commits.txt

# Check reflog for rewritten history
git reflog --all > ../reflog.txt

# List ALL branches including deleted remote refs
git branch -a -v > ../branches.txt

# Find suspicious large binary additions
git log --all --diff-filter=A --name-only --format="%H %ai" -- "*.so" "*.dll" "*.exe" "*.bin" > ../binary_additions.txt

# Check for GPG signature anomalies
git log --show-signature --format="%H %ai %aN" > ../signature_check.txt 2>&1

Evidence to collect (add via python SKILL_DIR/scripts/evidence-store.py add):

• Each dangling commit SHA → type: git
• Force-push evidence (reflog showing history rewrite) → type: git
• Unsigned commits from verified contributors → type: git
• Suspicious binary file additions → type: git

Reference: See recovery-techniques.md for accessing force-pushed commits.

Investigator 2: GitHub API Investigator

ROLE BOUNDARY: You query the GITHUB REST API ONLY. Do not run git commands locally.

Actions:

# Commits (paginated)
curl -s "https://api.github.com/repos/OWNER/REPO/commits?per_page=100" > api_commits.json

# Pull Requests including closed/deleted
curl -s "https://api.github.com/repos/OWNER/REPO/pulls?state=all&per_page=100" > api_prs.json

# Issues
curl -s "https://api.github.com/repos/OWNER/REPO/issues?state=all&per_page=100" > api_issues.json

# Contributors and collaborator changes
curl -s "https://api.github.com/repos/OWNER/REPO/contributors" > api_contributors.json

# Repository events (last 300)
curl -s "https://api.github.com/repos/OWNER/REPO/events?per_page=100" > api_events.json

# Check specific suspicious commit SHA details
curl -s "https://api.github.com/repos/OWNER/REPO/git/commits/SHA" > commit_detail.json

# Releases
curl -s "https://api.github.com/repos/OWNER/REPO/releases?per_page=100" > api_releases.json

# Check if a specific commit exists (force-pushed commits may 404 on commits/ but succeed on git/commits/)
curl -s "https://api.github.com/repos/OWNER/REPO/commits/SHA" | jq .sha

Cross-reference targets (flag discrepancies as evidence):

• PR exists in archive but missing from API → evidence of deletion
• Contributor in archive events but not in contributors list → evidence of permission revocation
• Commit in archive PushEvents but not in API commit list → evidence of force-push/deletion

Reference: See evidence-types.md for GH event types.

Investigator 3: Wayback Machine Investigator

ROLE BOUNDARY: You query the WAYBACK MACHINE CDX API ONLY. Do not use the GitHub API.

Goal: Recover deleted GitHub pages (READMEs, issues, PRs, releases, wiki pages).

Actions:

# Search for archived snapshots of the repo main page
curl -s "https://web.archive.org/cdx/search/cdx?url=github.com/OWNER/REPO&output=json&limit=100&from=YYYYMMDD&to=YYYYMMDD" > wayback_main.json

# Search for a specific deleted issue
curl -s "https://web.archive.org/cdx/search/cdx?url=github.com/OWNER/REPO/issues/NUM&output=json&limit=50" > wayback_issue_NUM.json

# Search for a specific deleted PR
curl -s "https://web.archive.org/cdx/search/cdx?url=github.com/OWNER/REPO/pull/NUM&output=json&limit=50" > wayback_pr_NUM.json

# Fetch the best snapshot of a page
# Use the Wayback Machine URL: https://web.archive.org/web/TIMESTAMP/ORIGINAL_URL
# Example: https://web.archive.org/web/20240101000000*/github.com/OWNER/REPO

# Advanced: Search for deleted releases/tags
curl -s "https://web.archive.org/cdx/search/cdx?url=github.com/OWNER/REPO/releases/tag/*&output=json" > wayback_tags.json

# Advanced: Search for historical wiki changes
curl -s "https://web.archive.org/cdx/search/cdx?url=github.com/OWNER/REPO/wiki/*&output=json" > wayback_wiki.json

Evidence to collect:

• Archived snapshots of deleted issues/PRs with their content
• Historical README versions showing changes
• Evidence of content present in archive but missing from current GitHub state

Reference: See github-archive-guide.md for CDX API parameters.

Investigator 4: GH Archive / BigQuery Investigator

ROLE BOUNDARY: You query GITHUB ARCHIVE via BIGQUERY ONLY. This is a tamper-proof record of all public GitHub events.

Prerequisites: Requires Google Cloud credentials with BigQuery access (gcloud auth application-default login). If unavailable, skip this investigator and note it in the report.

Cost Optimization Rules (MANDATORY):

1. ALWAYS run a --dry_run before every query to estimate cost.
2. Use _TABLE_SUFFIX to filter by date range and minimize scanned data.
3. Only SELECT the columns you need.
4. Add a LIMIT unless aggregating.

# Template: safe BigQuery query for PushEvents to OWNER/REPO
bq query --use_legacy_sql=false --dry_run "
SELECT created_at, actor.login, payload.commits, payload.before, payload.head,
       payload.size, payload.distinct_size
FROM \`githubarchive.month.*\`
WHERE _TABLE_SUFFIX BETWEEN 'YYYYMM' AND 'YYYYMM'
  AND type = 'PushEvent'
  AND repo.name = 'OWNER/REPO'
LIMIT 1000
"
# If cost is acceptable, re-run without --dry_run

# Detect force-pushes: zero-distinct_size PushEvents mean commits were force-erased
# payload.distinct_size = 0 AND payload.size > 0 → force push indicator

# Check for deleted branch events
bq query --use_legacy_sql=false "
SELECT created_at, actor.login, payload.ref, payload.ref_type
FROM \`githubarchive.month.*\`
WHERE _TABLE_SUFFIX BETWEEN 'YYYYMM' AND 'YYYYMM'
  AND type = 'DeleteEvent'
  AND repo.name = 'OWNER/REPO'
LIMIT 200
"

Evidence to collect:

• Force-push events (payload.size > 0, payload.distinct_size = 0)
• DeleteEvents for branches/tags
• WorkflowRunEvents for suspicious CI/CD automation
• PushEvents that precede a "gap" in the git log (evidence of rewrite)

Reference: See github-archive-guide.md for all 12 event types and query patterns.

Investigator 5: IOC Enrichment Investigator

ROLE BOUNDARY: You enrich EXISTING IOCs from Phase 1 using passive public sources ONLY. Do not execute any code from the target repository.

Actions:

• For each commit SHA: attempt recovery via direct GitHub URL (github.com/OWNER/REPO/commit/SHA.patch)
• For each domain/IP: check passive DNS, WHOIS records (via web_extract on public WHOIS services)
• For each package name: check npm/PyPI for matching malicious package reports
• For each actor username: check GitHub profile, contribution history, account age
• Recover force-pushed commits using 3 methods (see recovery-techniques.md)

Phase 3: Evidence Consolidation

After all investigators complete:

1. Run python SKILL_DIR/scripts/evidence-store.py --store evidence.json list to see all collected evidence.
2. For each piece of evidence, verify the content_sha256 hash matches the original source.
3. Group evidence by:
   • Timeline: Sort all timestamped evidence chronologically
   • Actor: Group by GitHub handle or email
   • IOC: Link evidence to the IOC it relates to
4. Identify discrepancies: items present in one source but absent in another (key deletion indicators).
5. Flag evidence as [VERIFIED] (confirmed from 2+ independent sources) or [UNVERIFIED] (single source only).

Phase 4: Hypothesis Formation

A hypothesis must:

• State a specific claim (e.g., "Actor X force-pushed to BRANCH on DATE to erase commit SHA")
• Cite at least 2 evidence IDs that support it (EV-XXXX, EV-YYYY)
• Identify what evidence would disprove it
• Be labeled [HYPOTHESIS] until validated

Common hypothesis templates (see investigation-templates.md):

• Maintainer Compromise: legitimate account used post-takeover to inject malicious code
• Dependency Confusion: package name squatting to intercept installs
• CI/CD Injection: malicious workflow changes to run code during builds
• Typosquatting: near-identical package name targeting misspellers
• Credential Leak: token/key accidentally committed then force-pushed to erase

For each hypothesis, spawn a delegate_task sub-agent to attempt to find disconfirming evidence before confirming.

Phase 5: Hypothesis Validation

The validator sub-agent MUST mechanically check:

1. For each hypothesis, extract all cited evidence IDs.
2. Verify each ID exists in evidence.json (hard failure if any ID is missing → hypothesis rejected as potentially fabricated).
3. Verify each [VERIFIED] piece of evidence was confirmed from 2+ sources.
4. Check logical consistency: does the timeline depicted by the evidence support the hypothesis?
5. Check for alternative explanations: could the same evidence pattern arise from a benign cause?

Output:

• VALIDATED: All evidence cited, verified, logically consistent, no plausible alternative explanation.
• INCONCLUSIVE: Evidence supports hypothesis but alternative explanations exist or evidence is insufficient.
• REJECTED: Missing evidence IDs, unverified evidence cited as fact, logical inconsistency detected.

Rejected hypotheses feed back into Phase 4 for refinement (max 3 iterations).

Phase 6: Final Report Generation

Populate investigation-report.md using the template in forensic-report.md.

Mandatory sections:

• Executive Summary: one-paragraph verdict (Compromised / Clean / Inconclusive) with confidence level
• Timeline: chronological reconstruction of all significant events with evidence citations
• Validated Hypotheses: each with status and supporting evidence IDs
• Evidence Registry: table of all EV-XXXX entries with source, type, and verification status
• IOC List: all extracted and enriched Indicators of Compromise
• Chain of Custody: how evidence was collected, from what sources, at what timestamps
• Recommendations: immediate mitigations if compromise detected; monitoring recommendations

Report rules:

• Every factual claim must have at least one [EV-XXXX] citation
• Executive Summary must state confidence level (High / Medium / Low)
• All secrets/credentials must be redacted to [REDACTED]

Phase 7: Completion

1. Run final evidence count: python SKILL_DIR/scripts/evidence-store.py --store evidence.json list
2. Archive the full investigation directory.
3. If compromise is confirmed:
   • List immediate mitigations (rotate credentials, pin dependency hashes, notify affected users)
   • Identify affected versions/packages
   • Note disclosure obligations (if a public package: coordinate with the package registry)
4. Present the final investigation-report.md to the user.

Ethical Use Guidelines

This skill is designed for defensive security investigation — protecting open-source software from supply chain attacks. It must not be used for:

• Harassment or stalking of contributors or maintainers
• Doxing — correlating GitHub activity to real identities for malicious purposes
• Competitive intelligence — investigating proprietary or internal repositories without authorization
• False accusations — publishing investigation results without validated evidence (see anti-hallucination guardrails)

Investigations should be conducted with the principle of minimal intrusion: collect only the evidence necessary to validate or refute the hypothesis. When publishing results, follow responsible disclosure practices and coordinate with affected maintainers before public disclosure.

If the investigation reveals a genuine compromise, follow the coordinated vulnerability disclosure process:

1. Notify the repository maintainers privately first
2. Allow reasonable time for remediation (typically 90 days)
3. Coordinate with package registries (npm, PyPI, etc.) if published packages are affected
4. File a CVE if appropriate

API Rate Limiting

GitHub REST API enforces rate limits that will interrupt large investigations if not managed.

Authenticated requests: 5,000/hour (requires GITHUB_TOKEN env var or gh CLI auth) Unauthenticated requests: 60/hour (unusable for investigations)

Best practices:

• Always authenticate: export GITHUB_TOKEN=ghp_... or use gh CLI (auto-authenticates)
• Use conditional requests (If-None-Match / If-Modified-Since headers) to avoid consuming quota on unchanged data
• For paginated endpoints, fetch all pages in sequence — don't parallelize against the same endpoint
• Check X-RateLimit-Remaining header; if below 100, pause for X-RateLimit-Reset timestamp
• BigQuery has its own quotas (10 TiB/day free tier) — always dry-run first
• Wayback Machine CDX API: no formal rate limit, but be courteous (1-2 req/sec max)

If rate-limited mid-investigation, record the partial results in the evidence store and note the limitation in the report.

Reference Materials

• github-archive-guide.md — BigQuery queries, CDX API, 12 event types
• evidence-types.md — IOC taxonomy, evidence source types, observation types
• recovery-techniques.md — Recovering deleted commits, PRs, issues
• investigation-templates.md — Pre-built hypothesis templates per attack type
• evidence-store.py — CLI tool for managing the evidence JSON store
• forensic-report.md — Structured report template