diff --git a/README.md b/README.md
index 12d1fef..18300b8 100644
--- a/README.md
+++ b/README.md
@@ -276,7 +276,7 @@ operator-entrypoints/wp-coding-agents-setup/setup.md
 | `--local` | Local machine mode. Skips server infrastructure. |
 | `--existing` | Add to an existing WordPress install. |
 | `--wp-path <path>` | WordPress root path. Implies `--existing`. |
-| `--agent-slug <slug>` | Override the Data Machine agent slug. |
+| `--agent-slug <slug>` | Override the Data Machine agent slug used by runtime instruction projections. Persisted for subsequent upgrades. |
 | `--kimaki-unit <unit>` | Target a Kimaki systemd instance, such as `kimaki-example.service`. |
 | `--kimaki-data-dir <path>` | Override that Kimaki instance's state directory. |
 | `--kimaki-lock-port <port>` | Override that Kimaki instance's lock port. |
diff --git a/lib/desired-state-reconciler.sh b/lib/desired-state-reconciler.sh
index 3dbb607..12b7a25 100644
--- a/lib/desired-state-reconciler.sh
+++ b/lib/desired-state-reconciler.sh
@@ -31,6 +31,7 @@ installation_profile_value() {
     studio) printf '%s' "$INSTALLATION_PROFILE_STUDIO" ;;
     source_mode) printf '%s' "$INSTALLATION_PROFILE_SOURCE_MODE" ;;
     runtime) printf '%s' "$INSTALLATION_PROFILE_RUNTIME" ;;
+    agent_slug) printf '%s' "$INSTALLATION_PROFILE_AGENT_SLUG" ;;
     install_chat) printf '%s' "$INSTALLATION_PROFILE_INSTALL_CHAT" ;;
     chat_bridge) printf '%s' "$INSTALLATION_PROFILE_CHAT_BRIDGE" ;;
     homeboy_mode) printf '%s' "$INSTALLATION_PROFILE_HOMEBOY_MODE" ;;
@@ -56,6 +57,7 @@ installation_profile_normalize() {
   INSTALLATION_PROFILE_STUDIO="${IS_STUDIO:-false}"
   INSTALLATION_PROFILE_SOURCE_MODE="${SOURCE_MODE:-workspace}"
   INSTALLATION_PROFILE_RUNTIME="${RUNTIME:-}"
+  INSTALLATION_PROFILE_AGENT_SLUG="${AGENT_SLUG:-}"
   INSTALLATION_PROFILE_INSTALL_CHAT="${INSTALL_CHAT:-true}"
   if [ "$INSTALLATION_PROFILE_INSTALL_CHAT" = true ]; then
     INSTALLATION_PROFILE_CHAT_BRIDGE="${CHAT_BRIDGE:-}"
@@ -125,7 +127,7 @@ installation_profile_write() {
     local key
     umask 077
     : > "$tmp"
-    for key in operation site_path local_mode external_wordpress studio source_mode runtime install_chat chat_bridge homeboy_mode workspace_repositories workspace_repository_clones components plugin_candidates; do
+    for key in operation site_path local_mode external_wordpress studio source_mode runtime agent_slug install_chat chat_bridge homeboy_mode workspace_repositories workspace_repository_clones components plugin_candidates; do
       printf '%s=%s\n' "$key" "$(installation_profile_value "$key")" >> "$tmp"
     done
     mv "$tmp" "$file"
@@ -146,6 +148,7 @@ installation_profile_load() {
     case "$key" in
       source_mode) [ "${SOURCE_MODE_EXPLICIT:-false}" = true ] || SOURCE_MODE="$value" ;;
       runtime) [ -n "${RUNTIME:-}" ] || RUNTIME="$value" ;;
+      agent_slug) [ -n "${AGENT_SLUG:-}" ] || AGENT_SLUG="$value" ;;
       install_chat)
         case "$value" in
           true|false) INSTALL_CHAT="$value" ;;
diff --git a/lib/runtime-guidance-desired-state.sh b/lib/runtime-guidance-desired-state.sh
index 44b219b..06e164b 100644
--- a/lib/runtime-guidance-desired-state.sh
+++ b/lib/runtime-guidance-desired-state.sh
@@ -127,6 +127,26 @@ runtime_guidance_desired_state_apply_instructions() {
   runtime_guidance_desired_state_apply_function runtime_generate_instructions
 }
 
+# Keep an existing managed Codex projection aligned with canonical AGENTS.md
+# even when another runtime is primary. The managed marker is explicit
+# authority; user-owned AGENTS.override.md files remain untouched.
+runtime_guidance_sync_managed_codex_projection() {
+  local projection="$SITE_PATH/AGENTS.override.md"
+  [ -f "$projection" ] || return 0
+  grep -Fq '<!-- WP_CODING_AGENTS_CODEX_OVERRIDE_START -->' "$projection" || return 0
+
+  local selected_runtime_file="${RUNTIME_FILE:-}"
+  # shellcheck disable=SC1090
+  source "$SCRIPT_DIR/runtimes/codex.sh"
+  runtime_discover_dm_paths || return $?
+  _codex_sync_override || return $?
+
+  if [ "${RUNTIME:-}" != codex ] && [ -n "$selected_runtime_file" ] && [ -f "$selected_runtime_file" ]; then
+    # shellcheck disable=SC1090
+    source "$selected_runtime_file"
+  fi
+}
+
 # apply and verify — use the shared plan executor so partial-record evidence
 # and future per-record verification stay consistent with other adapters.
 runtime_guidance_desired_state_apply() {
diff --git a/tests/installation-profile.sh b/tests/installation-profile.sh
index ac0342d..0290fcf 100644
--- a/tests/installation-profile.sh
+++ b/tests/installation-profile.sh
@@ -19,6 +19,7 @@ EXTERNAL_WORDPRESS=false
 IS_STUDIO=true
 SOURCE_MODE=workspace
 RUNTIME=opencode
+AGENT_SLUG=builder
 CHAT_BRIDGE=kimaki
 HOMEBOY_MODE=enabled
 WORKSPACE_REPOSITORIES="$WORKSPACE"
@@ -55,6 +56,7 @@ fi
 
 SOURCE_MODE=""
 RUNTIME=""
+AGENT_SLUG=""
 CHAT_BRIDGE=""
 HOMEBOY_MODE=auto
 WORKSPACE_REPOSITORIES=""
@@ -63,6 +65,7 @@ SOURCE_MODE_EXPLICIT=false
 installation_profile_load
 test "$SOURCE_MODE" = workspace
 test "$RUNTIME" = opencode
+test "$AGENT_SLUG" = builder
 test "$CHAT_BRIDGE" = kimaki
 test "$HOMEBOY_MODE" = enabled
 test "$WORKSPACE_REPOSITORIES" = "$WORKSPACE"
@@ -98,8 +101,10 @@ test "$INSTALL_CHAT" = true
 
 # Explicit command-line intent remains authoritative over persisted defaults.
 RUNTIME=codex
+AGENT_SLUG=reviewer
 installation_profile_load
 test "$RUNTIME" = codex
+test "$AGENT_SLUG" = reviewer
 
 # Disabled optional components round-trip as intent rather than being inferred
 # from whatever bridge binaries happen to be present during upgrade.
diff --git a/tests/runtime-guidance-desired-state.sh b/tests/runtime-guidance-desired-state.sh
index b98da3c..47f1208 100644
--- a/tests/runtime-guidance-desired-state.sh
+++ b/tests/runtime-guidance-desired-state.sh
@@ -92,4 +92,29 @@ reconciler_apply_plan
 assert_eq "$(<"$TRACE")" $'install\npaths\ncontext\nconfig\nhooks\ninstructions\nmcp' "runtime state survives its ordered component step"
 rm -f "$TRACE"
 
+# Canonical composition refreshes managed secondary-runtime projections while
+# preserving user-owned files and the selected runtime adapter.
+TRACE="$(mktemp)"
+SITE_PATH="$(mktemp -d)"
+SCRIPT_DIR="$(mktemp -d)"
+mkdir "$SCRIPT_DIR/runtimes"
+printf '%s\n' \
+  'runtime_discover_dm_paths() { printf "paths\\n" >> "$TRACE"; }' \
+  '_codex_sync_override() { printf "codex\\n" >> "$TRACE"; }' \
+  > "$SCRIPT_DIR/runtimes/codex.sh"
+printf '%s\n' \
+  'runtime_discover_dm_paths() { printf "selected\\n" >> "$TRACE"; }' \
+  > "$SCRIPT_DIR/runtimes/opencode.sh"
+RUNTIME=opencode
+RUNTIME_FILE="$SCRIPT_DIR/runtimes/opencode.sh"
+printf '<!-- WP_CODING_AGENTS_CODEX_OVERRIDE_START -->\n' > "$SITE_PATH/AGENTS.override.md"
+runtime_guidance_sync_managed_codex_projection
+assert_eq "$(<"$TRACE")" $'paths\ncodex' "managed Codex projection refreshes after canonical composition"
+runtime_discover_dm_paths
+assert_eq "$(<"$TRACE")" $'paths\ncodex\nselected' "selected runtime adapter is restored after projection refresh"
+printf '# user owned\n' > "$SITE_PATH/AGENTS.override.md"
+runtime_guidance_sync_managed_codex_projection
+assert_eq "$(<"$TRACE")" $'paths\ncodex\nselected' "user-owned Codex projection remains untouched"
+rm -rf "$SITE_PATH" "$SCRIPT_DIR" "$TRACE"
+
 echo "OK: runtime and guidance desired-state adapter"
diff --git a/upgrade.sh b/upgrade.sh
index 046179b..e528c4d 100755
--- a/upgrade.sh
+++ b/upgrade.sh
@@ -131,6 +131,7 @@ MULTISITE=false
 MULTISITE_TYPE="subdirectory"
 MODE="existing"
 RUNTIME=""
+AGENT_SLUG="${AGENT_SLUG:-}"
 DETECTED_RUNTIMES=()
 IS_STUDIO=false
 CHAT_BRIDGE=""
@@ -1475,6 +1476,9 @@ if _run_filter_active reconciliation; then
 fi
 sync_skills
 regenerate_agents_md
+if _run_filter_active agents-md; then
+  runtime_guidance_sync_managed_codex_projection
+fi
 sync_claude_code_runtime
 sync_runtime_signature
 sync_runtime_instructions