Security Scan

Security Scan

Used when a user wants to scan a pull request, commit, branch diff, working-tree patch, or repository for security vulnerabilities. Keep the scan phases separate and produce a final markdown report.

Phase Sequence

Keep these phases distinct and run them in linear order:

1. $threat-model
2. $finding-discovery
3. $validation
4. $attack-path-analysis
5. Generate final output

Treat this skill as the top-level orchestrator for the four skills plus the final report assembly step. Do not collapse the phases together.

For each phase:

1. Read that phase's skill.
2. Load only the inputs required for that phase.
3. Complete that phase's workflow and checklist.
4. Only then read the next phase's skill.

Do not read ahead into later-phase skills until the current phase has completed. Do not amortize effort across phases: complete each phase to the full depth expected by that phase before moving on.

Artifact Resolution

The path references in this skill are the default locations for this phase. If the user explicitly provides a different path for a required input or output, use the user-provided path instead of the corresponding default path referenced in this skill. If a required input is still missing, stop and ask the user for it before continuing. Use the shared scan artifact path conventions in ../../references/scan-artifacts.md.

Execution Plan

Follow this plan in order. Do not skip ahead to a later phase until the current phase has produced its intended output.

1. Resolve the scan target, repo_name, security_scans_dir, scan_id, scan_dir, and artifacts_dir using ../../references/scan-artifacts.md.
2. Run $threat-model first.

• Copy the repository-scoped threat model to the per-scan threat model path without alteration for auditability.
• Treat the per-scan threat model path as the source of truth threat model for later phases.

3. Run $finding-discovery as the second step, against the resolved diff and using the per-scan threat model as context.

• If discovery produces no technically plausible candidates in a diff-scoped scan, stop there, skip validation and attack-path analysis, and assemble the final markdown report immediately.
• In repository-wide scans, stop at discovery only when runtime_inventory.md exists and the coverage ledger has closed every applicable high-impact and seeded root-control row as suppressed, not_applicable, or deferred with exact reasons. Open, reportable, or unresolved seeded rows continue to validation even when they are not yet numbered as findings.

4. Run $validation as the third step, for each candidate that came out of discovery and, in repository-wide scans, each open, reportable, or deferred seeded/root-control ledger row that still needs closure.

• Pass the resolved scan scope, discovery notes, and candidate inventory to validation. Validation should preserve or suppress the provided instances; it should not independently decide whether a standalone single-candidate request should become diff-scoped or repository-wide.
• For repository-wide scans, the exhaustive file checklist and discovery coverage ledger are part of the validation input; the ledger is a coverage artifact, not just a findings tracker. Validation should preserve checked surfaces with not_applicable, suppressed, deferred, and reportable dispositions, and continue the ledger's high-impact sibling checks when needed rather than narrowing to one representative finding.
• As repository-wide rows are validated, keep the saved validation report current enough that reportable, suppressed, not_applicable, and deferred closure rows survive interruption or later phase summarization, including exact root-control file:line and seed-anchor file:line when distinct.

5. Run $attack-path-analysis as the fourth step, for findings and repository-wide validation closure rows that still need reportability, attack-path, and severity analysis after validation.
6. Assemble the final markdown report last using the final report path from ../../references/scan-artifacts.md and the outputs of the earlier phases: finding discovery, validation, attack path analysis.

Phase Scope

• Phase 1 (threat model generation) is repository-scope by default, unless the user explicitly asks for narrower scope or provides an authoritative threat model or sufficiently repository-specific security scan guidance such as AGENTS.md.
• For PR, commit, branch, and local-patch scans, Phase 2 onward (finding discovery, validation, attack path analysis) are diff-focused and should follow the changed code and its supporting files.
• For repository-wide scans, Phase 2 onward remain repository-wide. Before the $finding-discovery phase, read references/repository-wide-scan.md and every required reference it lists, then use them for finding discovery, validation, and attack path analysis.

Treat this asymmetry as intentional:

• use the diff to locate the scan target for later phases
• do not let the diff bias Phase 1 threat model generation, if applicable
• do not let the touched subsystem become the repository threat model unless the user explicitly asks for that narrower scope

Scan Target

Resolve the exact diff before starting:

• PR: compare base branch against current HEAD
• commit: scan the target commit against its parent or requested baseline
• branch diff: scan the requested merge-base to head range
• local patch: scan the working tree diff against the requested base
• repository-wide: scan the entire checked-out repository

For a repository-wide scan, treat the entire checked-out repository as the diff for the later phases of this workflow.

Diff-Scoped Sibling Coverage

For normal PR, commit, branch, and local-patch scans, stay diff-focused but preserve repeated vulnerable instances that are created or affected by the same changed pattern.

Diff scans should:

• start from the changed files and the supporting files needed to understand the changed behavior
• fan out from a changed route, handler, shared helper, guard, template pattern, query builder, serializer/deserializer, filesystem/network sink, config block, or wrapper to sibling instances that the diff also changes, newly reaches, or affects through the same modified shared dependency
• when the diff adds, removes, or reshapes a guard around an existing parser, deserializer, expression evaluator, filesystem/path helper, archive utility, or auth/authz helper, use the adjacent pre-existing sink/control as supporting context for the changed behavior; keep the candidate anchored to the changed guard or newly exposed path unless the user explicitly asks for wider instance expansion
• when a changed wrapper, guard, or API delegates to a shared parser/deserializer/path/archive/auth helper, keep both the wrapper call site and the underlying shared sink/control line addressable; do not replace the root sink/control evidence with wrapper-only evidence
• carry each vulnerable sibling instance through discovery and validation with its own affected location, source, closest control, sink, impact, and suppression evidence
• use unchanged siblings as context and negative controls, but report them only when the diff makes them newly vulnerable or changes the shared control or sink they depend on
• stop when the diff-linked pattern family is exhausted, rather than broadening into repository-wide enumeration

This keeps PR scans precise while avoiding the common failure mode where one representative route or sink hides additional vulnerable siblings introduced by the same patch.

Repository-Wide Exhaustive Mode

When the scan target is repository-wide, follow references/repository-wide-scan.md and every required reference it lists.

Use the per-scan artifact directory layout from ../../references/scan-artifacts.md.

Important:

Take any commit titles and descriptions with caution. They can be incomplete or misleading. Focus on the actual code and repository evidence.

Final Output

Assemble the final markdown report and Codex app review directives using references/final-report.md.

Hard Rules

• Keep the phases separate.
• Follow the execution plan in order.
• Use the tools to inspect the repository before making decisions.
• For repository-wide scans, do not equate broad sink counts with completed coverage. The coverage ledger must close each applicable high-impact shard row as reportable, suppressed, not_applicable, or deferred.
• Candidate ids are optional links from coverage rows to findings; a not_applicable, suppressed, or deferred row is still required when the surface was in scope.
• For repository-wide scans, the runtime inventory must exist as an artifact before discovery is considered complete, and the coverage ledger must be materially broader than the promoted candidate list.
• For repository-wide scans with CVE, GHSA, advisory, issue, release, or package-version identifiers, seed_research.md must exist before discovery is considered complete. It should record authoritative sources searched, candidate files/functions/classes/hunks, and failed lookup attempts. Missing seed research means advisory-led discovery is incomplete unless the scan explicitly states that no network/local-history source was available.
• In large repository-wide scans, checkpoint the runtime inventory and initial coverage ledger to disk before deep sink review or validation. A run that is interrupted after frontier mapping should still leave auditable coverage artifacts.
• In large monorepos, top product/runtime areas by file count or deployment significance must appear as ledger shards or be explicitly excluded with repository evidence; global sink counts and no top candidate surfaced do not close coverage.
• User/advisory/tag-seeded packages, class families, or vulnerability families remain open until the exact seeded row is closed as reportable, suppressed, not_applicable, or deferred. A neighboring same-family finding does not close the seeded row.
• For large repository-wide scans, make one reachability pass across every applicable high-impact shard before prolonged validation of any single shard. A row becomes a validation candidate only when it has a concrete entrypoint or privileged boundary, closest relevant control, sink or broken control, and plausible impact.
• Discovery is incomplete when a shard has a promoted finding but still has unclosed sibling packages, concrete implementations, or reusable root-control rows that could be independently vulnerable. Finish those rows or mark them explicitly deferred before final reporting.
• In large repositories, discovery is incomplete when it only follows the first obvious hotspot cluster and never checks a disjoint seeded/advisory or low-salience utility/control shard such as protocol/version helpers, central object-model helpers, reusable validators, or shared deserializer controls.
• Final assembly must start from reportable validation closure rows and surviving candidates. Do not drop a reportable seeded/root-control row because attack-path analysis or discovery spent more prose on a neighboring same-family finding.
• Final reporting is incomplete when a promoted high-impact finding's affected lines omit the concrete root-control file/line discovered or seeded during discovery, such as a codec, converter, parser feature setup, class filter, resource-path control, protocol state transition, or self-service update guard. Add the root-control affected line or explicitly suppress/defer it with exact counterevidence before finalizing.
• In repository-wide scans, preserve independently reachable sibling instances through final reporting. Repeated vulnerable templates, query builders, parser operations, auth/object endpoints, or shared-helper callers need separate finding entries, affected lines, and dispositions; put grouping in summary prose only after the individual instances are emitted.
• For query/parser injection, do not suppress syntax-control evidence solely because a later business check appears to limit impact. Carry the injection candidate until validation proves the exact query API and post-query guard defeat semantic change for that instance.
• If large-repository scope forces deferral, make the final report explicit about which deployed or privileged areas and vulnerability families remain deferred.
• Avoid destructive commands, interactive editors, and broad unbounded scans.
• Prefer targeted, reversible shell commands.
• For Phase 1 fallback threat model generation, produce a repository-level threat model that would still make sense for an unrelated diff in the same repository.
• Do not let the current scan target bias Phase 1 unless the user explicitly requests a target-scoped threat model.
• For later phases, stay grounded in repository evidence and the actual changed code.
• Do not emit a finding unless it survives the final policy-adjustment pass.