Merge pull request #1739 from astandrik/codex/fix-1689-codex-agents-cleanup

fix(codex): replace global guidance with an activation pointer

Author: DeusData

README.md

@@ -491,7 +491,7 @@ overwrite user-modified agents.
 | Agent | Activation | MCP config | Durable context / augmentation |
 |-------|------------|------------|--------------------------------|
 | Claude Code | Detected | `~/.claude.json` | Skill + three exact-tool graph agents; `SessionStart`, `SubagentStart`, non-blocking `PreToolUse` for `Grep`/`Glob`/`Bash`, and post-`Read` coverage |
-| Codex CLI | Detected | `$CODEX_HOME/config.toml` | `AGENTS.md`, skill, three read-only agents; `SessionStart` + `SubagentStart` |
+| Codex CLI | Detected | `$CODEX_HOME/config.toml` | Managed `AGENTS.md` activation pointer, skill, three read-only agents; `SessionStart` + `SubagentStart` |
 | Gemini CLI | Detected | `.gemini/settings.json` | `GEMINI.md`, three explicit read/graph-tool subagents; `BeforeTool`, `AfterTool` `read_file` coverage, and `SessionStart` |
 | Zed | Detected | platform `settings.json` (JSONC) | `AGENTS.md` + shared skill |
 | OpenCode | Detected | `$OPENCODE_CONFIG` or resolved global config | `AGENTS.md`, skill, three deny-by-default read-only agents; plugin adds grep/glob graph lookup, post-`read` coverage, first-tool-result session context, and post-compaction reinjection |
@@ -536,6 +536,11 @@ overwrite user-modified agents.
 | Oh My Pi (omp) | Detected | Effective agent directory (`OMP_PROFILE` / `PI_CODING_AGENT_DIR`; default `~/.omp/agent/mcp.json`) | Skill and three direct-MCP graph-tool subagents (Scout/Verify/Auditor); preserves user `AGENTS.md` |
 | Sourcegraph Cody | Explicit opt-in | Existing `$CBM_CODY_CONFIG_PATH` | MCP only |
 
+For Codex, install keeps only a tiny managed activation pointer in global
+`$CODEX_HOME/AGENTS.md`; all detailed behavior lives in the installed `codebase-memory` skill.
+Fresh installs create the pointer, upgrades replace the legacy full managed block while preserving
+all user-owned bytes, and uninstall removes only the managed pointer.
+
 ### Sessions, compaction, and subagents
 
 Hooks installed by this project are fail-open and context-only. Claude Code's

scripts/smoke-test.sh

@@ -144,11 +144,12 @@ run_no_crash() {
 
 TMPDIR=$(smoke_mktemp_dir)
 DRYRUN_HOME=""
+CODEX_LIFECYCLE_HOME=""
 # On MSYS2/Windows, convert POSIX path to native Windows path for the binary
 if command -v cygpath &>/dev/null; then
     TMPDIR=$(cygpath -m "$TMPDIR")
 fi
-trap 'smoke_rmtree "$TMPDIR" "${DRYRUN_HOME:-}"' EXIT
+trap 'smoke_rmtree "$TMPDIR" "${DRYRUN_HOME:-}" "${CODEX_LIFECYCLE_HOME:-}"' EXIT
 
 CLI_STDERR=$(smoke_mktemp_file)
 # 10 of the cli call sites assign directly (VAR=$(cli ...)). Under
@@ -1432,6 +1433,7 @@ echo '# Personal Rovo guidance' > "$ROVO_INSTRUCTIONS"
 PHASE8_INSTALL_RC=0
 PHASE8_INSTALL_LOG=$(smoke_mktemp_file)
 HOME="$FAKE_HOME" \
+  CODEX_HOME="$FAKE_HOME/.codex" \
   XDG_CONFIG_HOME="$FAKE_HOME/.config" \
   APPDATA="$FAKE_HOME/AppData/Roaming" \
   LOCALAPPDATA="$FAKE_HOME/AppData/Local" \
@@ -1704,12 +1706,139 @@ if ! grep -q 'existing_section' "$FAKE_HOME/.codex/config.toml"; then
 fi
 echo "OK 8f-h: Codex TOML (MCP + preserved existing)"
 
-# 8i: Codex instructions
-if [ ! -f "$FAKE_HOME/.codex/AGENTS.md" ] || ! grep -q 'codebase-memory-mcp' "$FAKE_HOME/.codex/AGENTS.md"; then
-  echo "FAIL 8i: Codex AGENTS.md missing"
-  exit 1
-fi
-echo "OK 8i: Codex instructions"
+# 8i: Codex keeps only a tiny global activation pointer; the installed skill
+# owns all detailed behavior. Exercise the complete lifecycle in a second HOME
+# so Codex-only reinstalls cannot perturb the all-agent fixture below.
+CODEX_POINTER_EXPECTED=$(smoke_mktemp_file)
+printf '%s\n' \
+  '<!-- codebase-memory-mcp:start -->' \
+  'For structural codebase exploration, use the installed `codebase-memory` skill.' \
+  '<!-- codebase-memory-mcp:end -->' > "$CODEX_POINTER_EXPECTED"
+if [ ! -f "$FAKE_HOME/.codex/AGENTS.md" ] ||
+   [ "$(smoke_file_sha256 "$FAKE_HOME/.codex/AGENTS.md")" != \
+     "$(smoke_file_sha256 "$CODEX_POINTER_EXPECTED")" ]; then
+  echo "FAIL 8i: fresh Codex install did not create the exact activation pointer"
+  exit 1
+fi
+
+CODEX_LIFECYCLE_HOME=$(smoke_mktemp_dir)
+CODEX_LIFECYCLE_ROOT="$CODEX_LIFECYCLE_HOME/.codex"
+CODEX_INSTRUCTIONS="$CODEX_LIFECYCLE_ROOT/AGENTS.md"
+mkdir -p "$CODEX_LIFECYCLE_ROOT"
+
+CODEX_FRESH_LOG=$(smoke_mktemp_file)
+HOME="$CODEX_LIFECYCLE_HOME" \
+  CODEX_HOME="$CODEX_LIFECYCLE_ROOT" \
+  XDG_CONFIG_HOME="$CODEX_LIFECYCLE_HOME/.config" \
+  APPDATA="$CODEX_LIFECYCLE_HOME/AppData/Roaming" \
+  LOCALAPPDATA="$CODEX_LIFECYCLE_HOME/AppData/Local" \
+  "$BINARY" install --skip-binary --clients=codex -y > "$CODEX_FRESH_LOG" 2>&1
+if [ ! -f "$CODEX_INSTRUCTIONS" ] ||
+   [ "$(smoke_file_sha256 "$CODEX_INSTRUCTIONS")" != \
+     "$(smoke_file_sha256 "$CODEX_POINTER_EXPECTED")" ] ||
+   ! grep -q '\[mcp_servers.codebase-memory-mcp\]' "$CODEX_LIFECYCLE_ROOT/config.toml" ||
+   ! grep -q 'search_graph' "$CODEX_LIFECYCLE_ROOT/skills/codebase-memory/SKILL.md" ||
+   [ ! -s "$CODEX_LIFECYCLE_ROOT/agents/codebase-memory-scout.toml" ] ||
+   [ ! -s "$CODEX_LIFECYCLE_ROOT/agents/codebase-memory.toml" ] ||
+   [ ! -s "$CODEX_LIFECYCLE_ROOT/agents/codebase-memory-auditor.toml" ] ||
+   ! grep -q 'SessionStart' "$CODEX_LIFECYCLE_ROOT/config.toml" ||
+   ! grep -q 'SubagentStart' "$CODEX_LIFECYCLE_ROOT/config.toml"; then
+  echo "FAIL 8i: isolated fresh Codex install lost the pointer or another surface"
+  exit 1
+fi
+
+printf '%s\n' \
+  '# Personal Codex guidance' \
+  '<!-- codebase-memory-mcp:start -->' \
+  'legacy managed guidance' \
+  '<!-- codebase-memory-mcp:end -->' \
+  '# Keep this line' > "$CODEX_INSTRUCTIONS"
+CODEX_EXPECTED_MIGRATED=$(smoke_mktemp_file)
+printf '%s\n' \
+  '# Personal Codex guidance' \
+  '<!-- codebase-memory-mcp:start -->' \
+  'For structural codebase exploration, use the installed `codebase-memory` skill.' \
+  '<!-- codebase-memory-mcp:end -->' \
+  '# Keep this line' > "$CODEX_EXPECTED_MIGRATED"
+CODEX_EXPECTED_USER=$(smoke_mktemp_file)
+printf '%s\n' '# Personal Codex guidance' '# Keep this line' > "$CODEX_EXPECTED_USER"
+CODEX_LEGACY_SHA=$(smoke_file_sha256 "$CODEX_INSTRUCTIONS")
+
+CODEX_PLAN=$(smoke_mktemp_file)
+HOME="$CODEX_LIFECYCLE_HOME" \
+  CODEX_HOME="$CODEX_LIFECYCLE_ROOT" \
+  XDG_CONFIG_HOME="$CODEX_LIFECYCLE_HOME/.config" \
+  APPDATA="$CODEX_LIFECYCLE_HOME/AppData/Roaming" \
+  LOCALAPPDATA="$CODEX_LIFECYCLE_HOME/AppData/Local" \
+  "$BINARY" install --plan --skip-binary --clients=codex > "$CODEX_PLAN"
+CODEX_INSTRUCTION_PATH=$(json_get "$CODEX_PLAN" \
+  "next((str(x) for x in d.get('instruction_files_planned', []) if str(x).replace('\\\\','/').endswith('/.codex/AGENTS.md')), '')")
+CODEX_CLEANUP_COUNT=$(json_get "$CODEX_PLAN" "len(d.get('cleanup_actions_planned', []))")
+if ! exact_path_match "$CODEX_INSTRUCTION_PATH" "$CODEX_INSTRUCTIONS" ||
+   [ "$CODEX_CLEANUP_COUNT" != "0" ] ||
+   [ "$CODEX_LEGACY_SHA" != "$(smoke_file_sha256 "$CODEX_INSTRUCTIONS")" ]; then
+  echo "FAIL 8i: Codex plan did not describe a non-mutating pointer upsert"
+  exit 1
+fi
+
+CODEX_DRY_LOG=$(smoke_mktemp_file)
+HOME="$CODEX_LIFECYCLE_HOME" \
+  CODEX_HOME="$CODEX_LIFECYCLE_ROOT" \
+  XDG_CONFIG_HOME="$CODEX_LIFECYCLE_HOME/.config" \
+  APPDATA="$CODEX_LIFECYCLE_HOME/AppData/Roaming" \
+  LOCALAPPDATA="$CODEX_LIFECYCLE_HOME/AppData/Local" \
+  "$BINARY" install --dry-run --skip-binary --clients=codex -y > "$CODEX_DRY_LOG" 2>&1
+if ! grep -q 'managed activation pointer' "$CODEX_DRY_LOG" ||
+   [ "$CODEX_LEGACY_SHA" != "$(smoke_file_sha256 "$CODEX_INSTRUCTIONS")" ]; then
+  echo "FAIL 8i: Codex dry-run did not preview a byte-identical pointer migration"
+  exit 1
+fi
+
+CODEX_MIGRATE_LOG=$(smoke_mktemp_file)
+HOME="$CODEX_LIFECYCLE_HOME" \
+  CODEX_HOME="$CODEX_LIFECYCLE_ROOT" \
+  XDG_CONFIG_HOME="$CODEX_LIFECYCLE_HOME/.config" \
+  APPDATA="$CODEX_LIFECYCLE_HOME/AppData/Roaming" \
+  LOCALAPPDATA="$CODEX_LIFECYCLE_HOME/AppData/Local" \
+  "$BINARY" install --skip-binary --clients=codex -y > "$CODEX_MIGRATE_LOG" 2>&1
+if [ ! -f "$CODEX_INSTRUCTIONS" ] ||
+   [ "$(smoke_file_sha256 "$CODEX_INSTRUCTIONS")" != \
+     "$(smoke_file_sha256 "$CODEX_EXPECTED_MIGRATED")" ]; then
+  echo "FAIL 8i: Codex migration did not replace only the legacy managed block"
+  exit 1
+fi
+
+HOME="$CODEX_LIFECYCLE_HOME" \
+  CODEX_HOME="$CODEX_LIFECYCLE_ROOT" \
+  XDG_CONFIG_HOME="$CODEX_LIFECYCLE_HOME/.config" \
+  APPDATA="$CODEX_LIFECYCLE_HOME/AppData/Roaming" \
+  LOCALAPPDATA="$CODEX_LIFECYCLE_HOME/AppData/Local" \
+  "$BINARY" install --skip-binary --clients=codex -y > /dev/null 2>&1
+if [ ! -f "$CODEX_INSTRUCTIONS" ] ||
+   [ "$(smoke_file_sha256 "$CODEX_INSTRUCTIONS")" != \
+     "$(smoke_file_sha256 "$CODEX_EXPECTED_MIGRATED")" ] ||
+   [ "$(grep -c '<!-- codebase-memory-mcp:start -->' "$CODEX_INSTRUCTIONS")" -ne 1 ]; then
+  echo "FAIL 8i: Codex reinstall changed or duplicated the activation pointer"
+  exit 1
+fi
+CODEX_UNINSTALL_LOG=$(smoke_mktemp_file)
+if ! HOME="$CODEX_LIFECYCLE_HOME" \
+     CODEX_HOME="$CODEX_LIFECYCLE_ROOT" \
+     XDG_CONFIG_HOME="$CODEX_LIFECYCLE_HOME/.config" \
+     APPDATA="$CODEX_LIFECYCLE_HOME/AppData/Roaming" \
+     LOCALAPPDATA="$CODEX_LIFECYCLE_HOME/AppData/Local" \
+     "$BINARY" uninstall -y -n > "$CODEX_UNINSTALL_LOG" 2>&1; then
+  echo "FAIL 8i: Codex uninstall returned nonzero"
+  cat "$CODEX_UNINSTALL_LOG"
+  exit 1
+fi
+if [ ! -f "$CODEX_INSTRUCTIONS" ] ||
+   [ "$(smoke_file_sha256 "$CODEX_INSTRUCTIONS")" != \
+     "$(smoke_file_sha256 "$CODEX_EXPECTED_USER")" ]; then
+  echo "FAIL 8i: Codex uninstall did not remove only the activation pointer"
+  exit 1
+fi
+echo "OK 8i: isolated Codex activation-pointer lifecycle"
 
 # 8j-l: Gemini MCP + hooks + merge
 CMD=$(json_get "$FAKE_HOME/.gemini/settings.json" "d['mcpServers']['codebase-memory-mcp']['command']")
@@ -2728,6 +2857,7 @@ if [[ "$BINARY" == *.exe ]]; then
   UNINSTALL_BINARY="$SELF_PATH"
 fi
 HOME="$FAKE_HOME" \
+  CODEX_HOME="$FAKE_HOME/.codex" \
   XDG_CONFIG_HOME="$FAKE_HOME/.config" \
   APPDATA="$FAKE_HOME/AppData/Roaming" \
   LOCALAPPDATA="$FAKE_HOME/AppData/Local" \

src/cli/cli.c

@@ -1393,18 +1393,7 @@ static const char skill_content[] =
     "5. `search_graph` results default to 50 per page — check `has_more` and use `offset`.\n";
 
 static const char codex_instructions_content[] =
-    "# Codebase Knowledge Graph\n"
-    "\n"
-    "This project uses codebase-memory-mcp to maintain a knowledge graph of the codebase.\n"
-    "Use the MCP tools to explore and understand the code:\n"
-    "\n"
-    "- `search_graph` — find functions, classes, routes by pattern\n"
-    "- `trace_path` — trace who calls a function or what it calls\n"
-    "- `get_code_snippet` — read function source code\n"
-    "- `query_graph` — run Cypher queries for complex patterns\n"
-    "- `get_architecture` — high-level project summary\n"
-    "\n"
-    "Always prefer graph tools over grep for code discovery.\n";
+    "For structural codebase exploration, use the installed `codebase-memory` skill.\n";
 
 /* Old skill names — cleaned up during install to remove stale directories. */
 static const char *old_skill_names[] = {
@@ -8054,6 +8043,24 @@ static bool install_generic_agent_config(const char *label, const char *binary_p
     return mcp_installed;
 }
 
+static bool install_codex_activation_pointer(const char *path, bool dry_run) {
+    if (!path) {
+        return false;
+    }
+    if (g_install_plan) {
+        plan_record("Codex CLI", "instructions", path);
+        return true;
+    }
+    return dry_run || cbm_upsert_instructions(path, codex_instructions_content) == CLI_OK;
+}
+
+static void report_codex_activation_pointer_install(const char *path, bool installed) {
+    printf("  instructions: %s (managed activation pointer)\n", path);
+    if (!installed) {
+        record_agent_config_error(false, "Codex CLI", "instructions_install", path);
+    }
+}
+
 static void install_windsurf_config(const char *binary_path, const char *config_path,
                                     const char *rules_path, bool dry_run) {
     if (g_install_plan) {
@@ -8997,6 +9004,8 @@ static void install_cli_agent_configs(const cbm_detected_agents_t *agents, const
         snprintf(ip, sizeof(ip), "%s/AGENTS.md", config_dir);
         snprintf(skills_dir, sizeof(skills_dir), "%s/skills", config_dir);
         snprintf(ap, sizeof(ap), "%s/agents/codebase-memory.toml", config_dir);
+        /* A broken hook config must not keep legacy full guidance active. */
+        bool pointer_installed = install_codex_activation_pointer(ip, dry_run);
         char command[CLI_BUF_8K];
         char command_windows[CLI_BUF_8K];
         char hooks_json[CLI_BUF_1K];
@@ -9024,10 +9033,16 @@ static void install_cli_agent_configs(const cbm_detected_agents_t *agents, const
             record_agent_config_error_with_reason(
                 false, "Codex CLI", commands_ok ? "hook_preflight" : "hook_command_build", cp,
                 reason);
+            if (!g_install_plan) {
+                report_codex_activation_pointer_install(ip, pointer_installed);
+            }
             goto codex_install_done;
         }
-        install_generic_agent_config("Codex CLI", binary_path, cp, ip, dry_run,
+        install_generic_agent_config("Codex CLI", binary_path, cp, NULL, dry_run,
                                      cbm_upsert_codex_mcp);
+        if (!g_install_plan) {
+            report_codex_activation_pointer_install(ip, pointer_installed);
+        }
         install_agent_skill("Codex CLI", skills_dir, force, dry_run);
         install_tiered_agent_profiles(
             (cbm_tiered_profile_set_t){
@@ -10953,6 +10968,17 @@ static void uninstall_agent_mcp_instr(mcp_uninstall_args_t paths, bool dry_run,
     }
 }
 
+static bool uninstall_codex_activation_pointer(const char *path, bool dry_run) {
+    return path && (dry_run || cbm_remove_instructions(path) == CLI_OK);
+}
+
+static void report_codex_activation_pointer_uninstall(const char *path, bool removed) {
+    printf("  instructions: removed managed activation pointer\n");
+    if (!removed) {
+        record_agent_config_error(true, "Codex CLI", "instructions_uninstall", path);
+    }
+}
+
 static void uninstall_agent_skill(const char *label, const char *skills_dir, bool dry_run) {
     int removed = cbm_remove_skills(skills_dir, dry_run);
     printf("  %s skill: %d removed\n", label, removed);
@@ -11387,6 +11413,7 @@ static void uninstall_cli_agents(const cbm_detected_agents_t *agents, const char
         snprintf(ip, sizeof(ip), "%s/AGENTS.md", config_dir);
         snprintf(skills_dir, sizeof(skills_dir), "%s/skills", config_dir);
         snprintf(ap, sizeof(ap), "%s/agents/codebase-memory.toml", config_dir);
+        bool pointer_removed = uninstall_codex_activation_pointer(ip, dry_run);
         cbm_agent_installed_binary_path(home, installed_binary, sizeof(installed_binary));
         char hook_command[CLI_BUF_8K];
         char hook_command_windows[CLI_BUF_8K];
@@ -11407,10 +11434,12 @@ static void uninstall_cli_agents(const cbm_detected_agents_t *agents, const char
                                      ? NULL
                                      : cbm_toml_codex_hook_failure_name(preflight_failure);
             record_agent_config_error_with_reason(true, "Codex CLI", "hook_preflight", cp, reason);
+            report_codex_activation_pointer_uninstall(ip, pointer_removed);
             goto codex_toml_done;
         }
-        uninstall_agent_mcp_instr((mcp_uninstall_args_t){"Codex CLI", cp, ip}, dry_run,
+        uninstall_agent_mcp_instr((mcp_uninstall_args_t){"Codex CLI", cp, NULL}, dry_run,
                                   cbm_remove_codex_mcp_owned);
+        report_codex_activation_pointer_uninstall(ip, pointer_removed);
         if (!dry_run &&
             cbm_reconcile_codex_hooks_command(cp, hook_command, hook_command_windows,
                                               CBM_TOML_CODEX_HOOK_REMOVE, false) != CLI_OK) {