feat(w9a): bulk-tag 25 primitives with taxonomy facets

8 capabilities (output/quality/safety/scope/tools) + 12 manifests +
5 roles. Consistent classification per W9-A rules.

Deprecated-alias stubs (tools::cargo-only-bash, tools::read-only)
skipped — no [gate]/[verify] sections.

facet-query results:
  kingdom=capability         → 11 hits (was 3)
  kingdom=capability gate    → 6 hits (was 2)
  kingdom=manifest           → 12 hits (was 0)

Roles tagged but not reachable by current facet_query (walker scans
_capabilities + _manifests). Forward-compat for walker extension.

cargo test -p kei-atom-discovery: 16/16 preserved.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

_capabilities/output/report-format/capability.toml

@@ -19,3 +19,16 @@ path = "text.md"
 rust-module = "verifies::output_report_format"
 run-mode = "worktree"
 when = "on-return"
+
+[taxonomy]
+kingdom = "capability"
+mechanism = "verify"
+domain = "output"
+layer = "agent-substrate"
+stage = "runtime"
+stability = "stable"
+language = "rust"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_capabilities/output/severity-grade/capability.toml

@@ -19,3 +19,16 @@ path = "text.md"
 rust-module = "verifies::output_severity_grade"
 run-mode = "worktree"
 when = "on-return"
+
+[taxonomy]
+kingdom = "capability"
+mechanism = "verify"
+domain = "output"
+layer = "agent-substrate"
+stage = "runtime"
+stability = "stable"
+language = "rust"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_capabilities/quality/constructor-pattern/capability.toml

@@ -19,3 +19,16 @@ path = "text.md"
 rust-module = "verifies::quality_constructor_pattern"
 run-mode = "worktree"
 when = "on-return"
+
+[taxonomy]
+kingdom = "capability"
+mechanism = "verify"
+domain = "quality"
+layer = "agent-substrate"
+stage = "runtime"
+stability = "stable"
+language = "rust"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_capabilities/quality/tests-green/capability.toml

@@ -19,3 +19,16 @@ path = "text.md"
 rust-module = "verifies::quality_tests_green"
 run-mode = "both"
 when = "on-return"
+
+[taxonomy]
+kingdom = "capability"
+mechanism = "verify"
+domain = "quality"
+layer = "agent-substrate"
+stage = "runtime"
+stability = "stable"
+language = "rust"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_capabilities/safety/no-dep-bump/capability.toml

@@ -24,3 +24,16 @@ severity = "block"
 rust-module = "verifies::safety_no_dep_bump"
 run-mode = "both"
 when = "on-return"
+
+[taxonomy]
+kingdom = "capability"
+mechanism = "gate"
+domain = "safety"
+layer = "agent-substrate"
+stage = "runtime"
+stability = "stable"
+language = "rust"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_capabilities/scope/files-denylist/capability.toml

@@ -24,3 +24,16 @@ severity = "block"
 rust-module = "verifies::scope_files_denylist"
 run-mode = "worktree"
 when = "on-return"
+
+[taxonomy]
+kingdom = "capability"
+mechanism = "gate"
+domain = "scope"
+layer = "agent-substrate"
+stage = "runtime"
+stability = "stable"
+language = "rust"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_capabilities/scope/files-whitelist/capability.toml

@@ -24,3 +24,16 @@ severity = "block"
 rust-module = "verifies::scope_files_whitelist"
 run-mode = "worktree"
 when = "on-return"
+
+[taxonomy]
+kingdom = "capability"
+mechanism = "gate"
+domain = "scope"
+layer = "agent-substrate"
+stage = "runtime"
+stability = "stable"
+language = "rust"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_capabilities/tools/deny-tools/capability.toml

@@ -19,3 +19,16 @@ path = "text.md"
 rust-module = "gates::tools_deny_tools"
 event = "PreToolUse:Edit|Write"
 severity = "block"
+
+[taxonomy]
+kingdom = "capability"
+mechanism = "gate"
+domain = "tools"
+layer = "agent-substrate"
+stage = "runtime"
+stability = "stable"
+language = "rust"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-architect.toml

@@ -98,3 +98,16 @@ trigger = "architectural claim needs hard reproduction (build graph, import grap
 # References (extra files beyond auto-included baseline/memory/project)
 [references]
 extra = []
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-code-implementer.toml

@@ -103,3 +103,16 @@ trigger = "structural decision (new module graph, cross-cutting refactor, contra
 extra = [
     "Background pattern: a real architectural-overlay case where audit fixes ballooned a file by over 50% of its original size — never patch, fix root formulas.",
 ]
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-cost-guardian.toml

@@ -92,3 +92,16 @@ extra = [
     "https://cloud.google.com/compute/all-pricing",
     "https://elevenlabs.io/pricing",
 ]
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-critic.toml

@@ -83,3 +83,16 @@ trigger = "anti-pattern is structural (new family, needs design review)"
 # References (extra files beyond auto-included baseline/memory/project)
 [references]
 extra = []
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-fal-ai-runner.toml

@@ -102,3 +102,16 @@ trigger = "anti-pattern sweep after batch — are prompts / generated assets con
 extra = [
     "https://fal.ai/pricing  (live pricing — WebFetch)",
 ]
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-infra-implementer.toml

@@ -98,3 +98,16 @@ extra = [
     "Background pattern: when several apps share one EC2/VPS host, host-level changes need cross-project sanity first; default SECRET_KEY + missing CSRF on touch-points must be fixed, not papered over.",
     "Background pattern: duplicate LaunchAgents or chatty sync daemons without log-silencing can fill disks with tens of GB — scan for duplicates before adding infra.",
 ]
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-ml-implementer.toml

@@ -102,3 +102,16 @@ extra = [
     "Background incident: a real cost-overrun (triple digits lost to unchecked Modal runs) motivates the Modal Protocol above.",
     "Background pattern: audit fixes can balloon a file by 50%+ when bolted on as overlays — fix at the root, not on top.",
 ]
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-ml-researcher.toml

@@ -81,3 +81,16 @@ trigger = "question is about ML-system architecture (node graph, data-flow, modu
 # References (extra files beyond auto-included baseline/memory/project)
 [references]
 extra = []
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-modal-runner.toml

@@ -102,3 +102,16 @@ trigger = "reported metrics must be verified before saving to `memory/{project}.
 extra = [
     "https://modal.com/pricing  (live pricing — WebFetch or user browser)",
 ]
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-researcher.toml

@@ -78,3 +78,16 @@ trigger = "findings suggest anti-pattern sweep or Constructor-Pattern violation
 # References (extra files beyond auto-included baseline/memory/project)
 [references]
 extra = []
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-security-auditor.toml

@@ -87,3 +87,16 @@ extra = [
     "https://cwe.mitre.org/top25/",
     "https://osv.dev/",
 ]
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_manifests/kei-validator.toml

@@ -80,3 +80,16 @@ trigger = "FALSE claim reveals broader pattern of unverified assertions in codeb
 # References (extra files beyond auto-included baseline/memory/project)
 [references]
 extra = []
+
+[taxonomy]
+kingdom = "manifest"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_roles/edit-local.toml

@@ -28,3 +28,16 @@ bash-patterns-allowed = ['^cargo( |$)', '^mkdir( |$)', '^rm -rf /tmp/']
 
 [escalation]
 policy = "ask-via-return"
+
+[taxonomy]
+kingdom = "role"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_roles/edit-shared.toml

@@ -21,3 +21,16 @@ bash-patterns-allowed = ['^cargo( |$)', '^mkdir( |$)', '^rm -rf /tmp/']
 [escalation]
 # Tightened vs edit-local: SSoT edits notify orchestrator on any unclear case
 policy = "orchestrator-notify"
+
+[taxonomy]
+kingdom = "role"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_roles/explorer.toml

@@ -16,3 +16,16 @@ bash-patterns-allowed = ['^cargo( |$)']
 
 [escalation]
 policy = "ask-via-return"
+
+[taxonomy]
+kingdom = "role"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_roles/git-ops.toml

@@ -20,3 +20,16 @@ bash-patterns-allowed = ['.*']
 [escalation]
 # Not reachable at runtime — orchestrator owns this context directly.
 policy = "fail-fast"
+
+[taxonomy]
+kingdom = "role"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"

_roles/read-only.toml

@@ -24,3 +24,16 @@ bash-patterns-allowed = []
 
 [escalation]
 policy = "ask-via-return"
+
+[taxonomy]
+kingdom = "role"
+mechanism = "compose"
+domain = "agent"
+layer = "agent-substrate"
+stage = "design-time"
+stability = "stable"
+language = "toml"
+
+[lineage]
+creator = "ag-orchestrator-human"
+created = "2026-04-23"