diff --git a/docs/ai-environment-boundary.md b/docs/ai-environment-boundary.md
index 559d144..8f6089f 100644
--- a/docs/ai-environment-boundary.md
+++ b/docs/ai-environment-boundary.md
@@ -82,7 +82,7 @@ AI skills / agents project は、`dotfiles` の policy を前提に動く。poli
 - `dotfiles` は AI skills / agents project の path を表示してよい。
 - `dotfiles` は AI skills / agents project を自動更新しない。
 - `dotfiles` は AI skills / agents project の secret を読まない。
-- `dotfiles` の `doctor` は `~/src/agent/agent-tools`(既定。非標準な checkout 先は `AGENT_TOOLS` env で override 可)の presence を report する。status(`scripts/status.sh --json`、report-only、`contract_version: 2`)の読み取りは別 repo のコード実行になるため、`enableAgentToolsStatus` capability での明示 opt-in 時のみ実行し、安全な summary(`conflict` / `stale` / 失敗 check 等は warning)を出す(Issue #7)。clone / pull / sync は一切しない。
+- `dotfiles` の `doctor` は `~/src/agent/agent-tools`(既定。非標準な checkout 先は `AGENT_TOOLS` env で override 可)の presence を report する。status(`scripts/status.sh --json`、report-only、`contract_version: 3`)の読み取りは別 repo のコード実行になるため、`enableAgentToolsStatus` capability での明示 opt-in 時のみ実行し、安全な summary(`conflict` / `stale` / `deployed_but_inactive` / 失敗 check 等は warning)を出す(Issue #7、v3 追従は #194)。clone / pull / sync は一切しない。
 - AI skills / agents project は `dotfiles` の capability を前提条件として参照してよい。
 - AI skills / agents project が install、network tunnel、secret access を必要とする場合は、`dotfiles` 側の capability と approval policy に従う。
 
diff --git a/scripts/doctor.sh b/scripts/doctor.sh
index 1b8cf00..531733d 100755
--- a/scripts/doctor.sh
+++ b/scripts/doctor.sh
@@ -670,7 +670,7 @@ section "agent-tools (report-only)"
 # (executing code from another repo) is opt-in via enableAgentToolsStatus
 # so doctor's no-side-effects invariant is never delegated implicitly.
 # See docs/ai-environment-boundary.md and the agent-tools
-# status-manifest-contract (contract_version 2).
+# status-manifest-contract (contract_version 3).
 # The expected path defaults to the dotfiles directory convention
 # (~/src/agent/agent-tools) but is overridable via the AGENT_TOOLS env so a
 # non-standard checkout can still be reported. presence only; never cloned.
@@ -695,10 +695,10 @@ else
     # the JSON is malformed (a failed substitution would trip set -e).
     sj() { printf '%s' "$status_json" | yq -p json "$1" 2>/dev/null || true; }
     contract_version="$(sj '.contract_version // ""')"
-    if [[ "$contract_version" != "2" ]]; then
-      warn "agent-tools status contract_version=${contract_version:-unknown}, expected 2 (not interpreting fields)"
+    if [[ "$contract_version" != "3" ]]; then
+      warn "agent-tools status contract_version=${contract_version:-unknown}, expected 3 (not interpreting fields)"
     else
-      ok "agent-tools present; status contract v2"
+      ok "agent-tools present; status contract v3"
 
       if [[ "$(sj '.repo.clean // false')" == "true" ]]; then
         ok "agent-tools working tree clean"
@@ -741,6 +741,10 @@ else
       if [[ "$(sj '[.sync_targets[]? | select(.state == "stale")] | length')" != "0" ]]; then
         warn "agent-tools has stale sync targets (generated artifact newer than target)"
       fi
+      # v3 (#194): gated-but-still-deployed leftovers are cleanup candidates.
+      if [[ "$(sj '[.sync_targets[]? | select(.state == "deployed_but_inactive")] | length')" != "0" ]]; then
+        warn "agent-tools has deployed-but-inactive sync targets (gated entries still on disk; clean up or re-approve)"
+      fi
     fi
     unset -f sj
   fi
diff --git a/scripts/test-doctor.sh b/scripts/test-doctor.sh
index 3db8098..0ff9b19 100755
--- a/scripts/test-doctor.sh
+++ b/scripts/test-doctor.sh
@@ -146,7 +146,7 @@ agent_marker="$agent_dir/ran-marker"
 mkdir -p "$agent_scripts"
 # Root-pinning fake (see write_root_pinned_status_sh): regression for #73.
 write_root_pinned_status_sh "$agent_scripts/status.sh" \
-  '{"contract_version":2,"repo":{"present":true,"clean":true},"assets":{"total":1,"manifest_errors":0},"checks":{"manifest_validation":"pass","prompt_injection_static":"pass"},"generated":{"total":1,"stale":0},"register":{"catalog_present":true,"registered":1,"human_review_required":0,"unsupported":0},"sync_targets":[{"tool":"codex","name":"x","state":"conflict"}]}'
+  '{"contract_version":3,"repo":{"present":true,"clean":true},"assets":{"total":1,"manifest_errors":0},"checks":{"manifest_validation":"pass","prompt_injection_static":"pass"},"generated":{"total":1,"stale":0},"register":{"catalog_present":true,"registered":1,"human_review_required":0,"unsupported":0},"sync_targets":[{"tool":"codex","name":"x","state":"conflict"},{"tool":"codex","name":"y","state":"deployed_but_inactive"}]}'
 
 # A) Opt-in disabled: present but status.sh must not run. Force the capability
 #    off in a throwaway copy so the test is independent of the real default
@@ -178,9 +178,10 @@ set_capability_all "$optin_root" enableAgentToolsStatus true
 # B) Opt-in enabled: status.sh runs, summary shown, conflict flagged.
 rm -f "$agent_marker"
 if at_out="$(HOME="$fixture_home" "$optin_root/scripts/doctor.sh" personal 2>&1)"; then
-  if grep -Fq "agent-tools present; status contract v2" <<< "$at_out" \
-    && grep -Fq "sync conflicts" <<< "$at_out" && [[ -e "$agent_marker" ]]; then
-    ok "test passed: opt-in runs status.sh and summarizes (conflict flagged)"
+  if grep -Fq "agent-tools present; status contract v3" <<< "$at_out" \
+    && grep -Fq "sync conflicts" <<< "$at_out" \
+    && grep -Fq "deployed-but-inactive sync targets" <<< "$at_out" && [[ -e "$agent_marker" ]]; then
+    ok "test passed: opt-in runs status.sh and summarizes (conflict + inactive leftovers flagged)"
   else
     printf '%s\n' "$at_out" >&2
     fail "test failed: opt-in summary/conflict/marker missing"
@@ -193,16 +194,21 @@ else
 fi
 
 # C) Opt-in + unknown contract version: not interpreted, still exit 0.
+# Sentinel fields prove fail-closed: a doctor that warns but still interprets
+# fields would emit the summary lines below, so their absence is asserted too.
 cat > "$agent_scripts/status.sh" <<'SH'
 #!/bin/sh
 json=0
 for a in "$@"; do [ "$a" = "--json" ] && json=1; done
 [ "$json" = 1 ] || exit 1
-echo '{"contract_version":99}'
+echo '{"contract_version":99,"repo":{"present":true,"clean":true},"sync_targets":[{"tool":"codex","name":"x","state":"conflict"},{"tool":"codex","name":"y","state":"deployed_but_inactive"}]}'
 SH
 chmod +x "$agent_scripts/status.sh"
 if at_out="$(HOME="$fixture_home" "$optin_root/scripts/doctor.sh" personal 2>&1)"; then
-  if grep -Fq "expected 2 (not interpreting fields)" <<< "$at_out"; then
+  if grep -Fq "expected 3 (not interpreting fields)" <<< "$at_out" \
+    && ! grep -Fq "agent-tools working tree clean" <<< "$at_out" \
+    && ! grep -Fq "sync conflicts" <<< "$at_out" \
+    && ! grep -Fq "deployed-but-inactive sync targets" <<< "$at_out"; then
     ok "test passed: unknown contract version is not interpreted (exit 0)"
   else
     printf '%s\n' "$at_out" >&2
@@ -284,7 +290,7 @@ else
 fi
 
 # AT-override) AGENT_TOOLS overrides the expected path (issue #71). The
-#    default ~/src/agent/agent-tools is absent (removed in E), so a v2 summary
+#    default ~/src/agent/agent-tools is absent (removed in E), so a v3 summary
 #    plus the run marker proves doctor read the overridden checkout.
 override_dir="$fixture_home/custom/agent-tools"
 override_scripts="$override_dir/scripts"
@@ -293,10 +299,10 @@ mkdir -p "$override_scripts"
 # Same root-pinning contract as the default-path fake: doctor must pass
 # --root equal to the AGENT_TOOLS-overridden checkout (#71 + #73).
 write_root_pinned_status_sh "$override_scripts/status.sh" \
-  '{"contract_version":2,"repo":{"present":true,"clean":true},"assets":{"total":0,"manifest_errors":0},"checks":{"manifest_validation":"pass","prompt_injection_static":"pass"},"generated":{"total":0,"stale":0},"register":{"catalog_present":false,"registered":0,"human_review_required":0,"unsupported":0},"sync_targets":[]}'
+  '{"contract_version":3,"repo":{"present":true,"clean":true},"assets":{"total":0,"manifest_errors":0},"checks":{"manifest_validation":"pass","prompt_injection_static":"pass"},"generated":{"total":0,"stale":0},"register":{"catalog_present":false,"registered":0,"human_review_required":0,"unsupported":0},"sync_targets":[]}'
 rm -f "$override_marker"
 if at_out="$(HOME="$fixture_home" AGENT_TOOLS="$override_dir" "$optin_root/scripts/doctor.sh" personal 2>&1)"; then
-  if grep -Fq "agent-tools present; status contract v2" <<< "$at_out" && [[ -e "$override_marker" ]]; then
+  if grep -Fq "agent-tools present; status contract v3" <<< "$at_out" && [[ -e "$override_marker" ]]; then
     ok "test passed: AGENT_TOOLS overrides the expected path"
   else
     printf '%s\n' "$at_out" >&2