Agent pack: structured query verbs, drop GQL skills and --with-commands

[sshaaf]

Summary

Agent pack / structured query (earlier on branch)

• Prefer mmap structured verbs (find / callers / relations / inventory / status / rules run) for agent workflows; remove GQL from skills and the agent pack.
• Drop rgctl install --with-commands (skills + optional --with-policy only; install JSON schema_version 3).
• Migration search primitives: annotation find, import-prefix inventory, session status, Kantra rules run; related skill / encyclopedia / website updates.
• Constrained discover limits, ingest hot-path / spill / tracker work, and release tooling.

OpenSpec: OSV deps → declarative taint → reachability / OpenVEX

End-to-end agent path:

vuln triage → deps check → find/callers --package → blast-radius --classify-boundary
  → taint --sink … --source external → vuln analyze → OpenVEX

1. add-osv-deps-supply-chain

• rgctl vuln triage --osv — parse via osv 0.3 schema crate
• rgctl deps check --osv — manifests + opt-in --include-jars / --include-node-modules
• Version engines: Maven (incl. -rhlw-), Cargo, npm, Go
• Verdicts: not_affected | affected_candidate
• CoolStore fixtures (jackson / xalan); skill workflows/vuln.md; json-api §18

2. add-declarative-taint-rules (#16)

• TaintRuleSet loads YAML packs, compiles once per language, first-match-wins
• Tier‑1 packs under crates/rgctl-analysis/rules/taint/ — hardcoded detect_*_patterns removed
• CWE catalog YAML; default_cwe_patterns() reads it
• --taint-rules PATH + .rgctl/taint-rules.d/ (built-in < project < CLI); with_overlays for OSV sinks
• Taint remains opt-in (--with-taint)

3. add-vuln-reachability-vex

• Package resolver (Maven/npm/Cargo/Go/PyPI + stubs; xalan table; runtime_bundled)
• find / callers --package + bundled_presence honesty; callers --methods
• Boundary catalogs (Java/Jakarta + Python); blast-radius --classify-boundary
• rgctl taint --sink … --source external (CFG required; declarative overlays)
• rgctl vuln analyze --osv … → OpenVEX (openvex crate)
• CoolStore A/B release smoke + extended vuln workflow

Live CoolStore validation (before → after)

Probe	Before (3 OpenSpecs)	After
P1 dep match	🔧 Python zipfile workaround	✅ NATIVE
P2 namespace resolve	🔧 manual gav-namespace-map.json	✅ NATIVE
P4 facade callers	⚠️ partial	✅ NATIVE
P6 taint	⚠️ partial (manual file+line+variable)	✅ NATIVE
Gate	PASS 4/6	PASS 7/7

• rgctl vuln analyze → OpenVEX in 46ms for both scenarios
• Every probe: ✅ NATIVE

Validated verdicts

• Xalan: not_affected / component_not_present — 2-phase fast exit
• Jackson (bundled JAR at 2.13.5): not_affected / vulnerable_code_not_in_execute_path — 5-phase full pipeline; sink-first taint confirmed no external→readValue path

Known follow-ups (not blocking)

1. discover --with-cfg --with-taint needed for PDG-backed taint confidence (cfg_available=false today)
2. Xalan’s JDK-bundled path (javax.xml.transform.*) not yet surfaced in find --package resolution output

Test plan

• CoolStore live gate PASS 7/7 (native probes; OpenVEX ~46ms)
• cargo test -p rgctl-security --lib
• cargo test -p rgctl-analysis --lib taint boundary
• cargo test -p rgctl-agent-pack-codegen
• cargo build --release --bin rgctl
• cargo test --release --test osv_deps_release_smoke -- --ignored --nocapture
• cargo test --release --test taint_rules_release_smoke -- --ignored --nocapture
• cargo test --release --test vuln_reachability_release_smoke -- --ignored --nocapture (needs example/coolstore)
• Spot-check: vuln triage / deps check / vuln analyze --include-jars lib on CoolStore; taint --help; no new rgctl-vuln skill dirs