@zalom/plastic 1.9.0 → 1.11.0

package/scripts/lib/doctor_core.rb

@@ -0,0 +1,1087 @@
+# encoding: UTF-8
+# frozen_string_literal: true
+
+# Core half of the Plastic doctor (intent 228). Holds run_core_checks and every
+# method, constant and require it reaches, and nothing else, so the SessionStart
+# hook can load the boot check without pulling in the full 3,100-line diagnostic
+# engine. scripts/doctor.rb requires this file and reopens the same class to add
+# the store, conventions, intent and CLI halves, so Doctor stays one class with
+# one public surface and one definition of which checks are core (intent 36a).
+
+require "json"
+require "yaml"
+require "time"
+require "digest"
+require "rubygems"
+
+require_relative "hook_registry"
+
+class Doctor
+  DEFAULT_PLASTIC_HOME = File.join(Dir.home, ".plastic")
+
+  DEFAULT_AGENTS = {
+    "claude" => { name: "Claude Code", dir: File.join(Dir.home, ".claude") },
+    "codex"  => { name: "Codex CLI",   dir: File.join(Dir.home, ".agents"),
+                  home_dir: File.join(Dir.home, ".codex") },
+    "hermes" => { name: "Hermes",      dir: File.join(Dir.home, ".hermes") },
+  }.freeze
+
+  CLAUDE_HOOK_EVENTS = %w[SessionStart PreCompact PostToolUse UserPromptSubmit].freeze
+
+  # Launchers the installer places in the agent's hooks dir that are NOT hooks
+  # (intent 204): plastic-statusline is the settings["statusLine"] command, wired
+  # outside HookRegistry.events entirely, so it must be excluded from the
+  # orphan-launcher scan below or a correct install would report a false orphan.
+  CLAUDE_NON_HOOK_LAUNCHERS = %w[plastic-statusline].freeze
+
+  REQUIRED_SCRIPTS = %w[
+    folgezettel-id
+    read-config
+    hook-session-start
+    hook-continue
+    hook-future-intent-check
+    hook-gate-check
+    validate-intent
+    doctor.rb
+  ].freeze
+
+  # The apply_patch PreToolUse veto only fires from Codex v0.123.0 onward
+  # (PR #18391, "emit hooks for apply_patch edits"). Below it the veto
+  # silently no-ops (intent 184).
+  CODEX_HOOKS_FLOOR = "0.123.0"
+
+  attr_reader :plastic_home, :agents
+
+  # Testable shell-out default, mirroring QmdSync.default_runner: a real
+  # Open3.capture3 call in production, swappable for a fake in tests so no
+  # test needs a real codex binary or a PATH mutation.
+  def self.default_runner
+    lambda do |args|
+      require "open3"
+      out, _err, status = Open3.capture3("codex", *args)
+      [out, status.success?]
+    rescue Errno::ENOENT
+      ["", false] # codex not on PATH: undetectable, fail open
+    end
+  end
+
+  def initialize(plastic_home: DEFAULT_PLASTIC_HOME, agents: DEFAULT_AGENTS,
+                  runner: Doctor.default_runner)
+    @plastic_home = plastic_home
+    @agents = agents
+    @runner = runner
+  end
+
+  # --- Utility helpers ---
+
+  def read_version
+    version_path = File.join(plastic_home, "VERSION")
+    return nil unless File.exist?(version_path)
+
+    File.read(version_path).strip
+  end
+
+  def read_json_safe(path)
+    return nil unless File.exist?(path)
+
+    JSON.parse(File.read(path))
+  rescue JSON::ParserError
+    content = File.read(path).gsub(%r{//[^\n]*}, "").gsub(/,(\s*[}\]])/, '\1')
+    JSON.parse(content)
+  rescue
+    nil
+  end
+
+  def load_yaml_safe(path)
+    return nil unless File.exist?(path)
+
+    YAML.safe_load(File.read(path)) || {}
+  rescue => e
+    $stderr.puts "Warning: failed to parse #{path}: #{e.message}"
+    nil
+  end
+
+  def tilde(path)
+    path.sub(Dir.home, "~")
+  end
+
+  def check(category:, name:, status:, message:, details: [], fixable: false, fix_hint: nil)
+    result = {
+      category: category,
+      name: name,
+      status: status,
+      message: message,
+      details: details,
+      fixable: fixable,
+    }
+    result[:fix_hint] = fix_hint if fix_hint
+    result
+  end
+
+  def check_global_store_available
+    checks = []
+
+    if File.directory?(plastic_home)
+      checks << check(
+        category: "global_store", name: "global_store_reachable", status: "pass",
+        message: "Global store directory reachable at #{tilde(plastic_home)}"
+      )
+    else
+      checks << check(
+        category: "global_store", name: "global_store_reachable", status: "fail",
+        message: "Global store directory not found at #{tilde(plastic_home)}",
+        fixable: true, fix_hint: "Run the Plastic installer to bootstrap the store"
+      )
+      return checks
+    end
+
+    index_path = File.join(plastic_home, "INDEX.md")
+    if File.exist?(index_path)
+      checks << check(
+        category: "global_store", name: "global_index_reachable", status: "pass",
+        message: "INDEX.md exists"
+      )
+    else
+      checks << check(
+        category: "global_store", name: "global_index_reachable", status: "fail",
+        message: "INDEX.md not found at #{tilde(index_path)}",
+        fixable: true, fix_hint: "Run the Plastic installer to bootstrap the store"
+      )
+    end
+
+    checks
+  end
+
+  def check_agent_registration(agent_key)
+    checks = []
+    config = agents[agent_key]
+    agent_dir = config[:dir]
+
+    unless File.directory?(agent_dir)
+      checks << check(
+        category: "agent_registration", name: "agent_dir_exists", status: "fail",
+        message: "Agent directory #{tilde(agent_dir)} not found — #{config[:name]} may not be installed",
+        fixable: false
+      )
+      return checks
+    end
+
+    case agent_key
+    when "claude"
+      checks += check_claude_registration(agent_dir)
+    when "codex"
+      checks += check_codex_registration(agent_key, agent_dir)
+    else
+      checks += check_generic_agent_registration(agent_key, agent_dir)
+    end
+
+    checks
+  end
+
+  def check_claude_registration(agent_dir)
+    checks = []
+    hooks_dir = File.join(agent_dir, "hooks")
+
+    # Derived from HookRegistry.events (intent 204), not a hand-kept list, so
+    # every registered hook (all 15, including the enforcement gates) is checked.
+    expected_launchers = HookRegistry.claude_launcher_names
+
+    # hooks_exist
+    missing_hooks = expected_launchers.reject { |h| File.exist?(File.join(hooks_dir, h)) }
+
+    if missing_hooks.empty?
+      checks << check(
+        category: "agent_registration", name: "hooks_exist", status: "pass",
+        message: "All #{expected_launchers.size} expected hook scripts exist"
+      )
+    else
+      checks << check(
+        category: "agent_registration", name: "hooks_exist", status: "fail",
+        message: "#{missing_hooks.size} hook script(s) missing",
+        details: missing_hooks.map { |h| "#{tilde(hooks_dir)}/#{h}" },
+        fixable: true, fix_hint: "Re-run the Plastic installer: npx @zalom/plastic@latest --claude"
+      )
+    end
+
+    # hooks_executable
+    existing_hooks = expected_launchers
+      .map { |h| File.join(hooks_dir, h) }
+      .select { |p| File.exist?(p) }
+
+    non_executable = existing_hooks.reject { |p| File.executable?(p) }
+
+    if non_executable.empty?
+      checks << check(
+        category: "agent_registration", name: "hooks_executable", status: "pass",
+        message: "All existing hook scripts are executable"
+      )
+    else
+      checks << check(
+        category: "agent_registration", name: "hooks_executable", status: "fail",
+        message: "#{non_executable.size} hook script(s) not executable",
+        details: non_executable.map { |p| tilde(p) },
+        fixable: true, fix_hint: "chmod +x on the listed files"
+      )
+    end
+
+    # hooks_no_orphans: the mirror of hooks_exist. A plastic-* launcher on disk
+    # that HookRegistry does not know about is dead code the next reader would
+    # trust as live (the same drift class as a missing launcher, just facing
+    # the other way). plastic-statusline is a legitimate non-hook installer
+    # artifact (see CLAUDE_NON_HOOK_LAUNCHERS) and is excluded here.
+    present_launchers = Dir.glob(File.join(hooks_dir, "plastic-*")).map { |p| File.basename(p) }
+    orphans = (present_launchers - expected_launchers - CLAUDE_NON_HOOK_LAUNCHERS).sort
+
+    if orphans.empty?
+      checks << check(
+        category: "agent_registration", name: "hooks_no_orphans", status: "pass",
+        message: "No orphaned hook launchers in #{tilde(hooks_dir)}"
+      )
+    else
+      checks << check(
+        category: "agent_registration", name: "hooks_no_orphans", status: "warn",
+        message: "#{orphans.size} hook launcher(s) on disk are not registered in HookRegistry",
+        details: orphans.map { |h| "#{tilde(hooks_dir)}/#{h}" },
+        fixable: true,
+        fix_hint: "Re-run the Plastic installer: npx @zalom/plastic@latest --claude (prunes stale launchers)"
+      )
+    end
+
+    # claude_hooks_implemented (intent 244): the edit-path gates now live as
+    # branches inside one dispatcher (scripts/hook-edit-gates), which is
+    # exactly the shape that let links-gate ship registered and dead on
+    # Codex (intent 200's failure class, one level up).
+    checks << claude_hooks_implemented_check
+
+    # hooks_registered — settings.json has Plastic hooks for required events
+    settings_path = File.join(agent_dir, "settings.json")
+    settings = read_json_safe(settings_path)
+
+    if settings.nil?
+      checks << check(
+        category: "agent_registration", name: "hooks_registered", status: "fail",
+        message: "Cannot read #{tilde(settings_path)} — file missing or invalid",
+        fixable: true, fix_hint: "Re-run the Plastic installer: npx @zalom/plastic@latest --claude"
+      )
+    else
+      hooks = settings["hooks"] || {}
+      missing_events = CLAUDE_HOOK_EVENTS.reject do |event|
+        groups = hooks[event]
+        next false unless groups.is_a?(Array)
+
+        groups.any? do |group|
+          group.is_a?(Hash) && group["hooks"].is_a?(Array) &&
+            group["hooks"].any? { |h| h["command"].to_s.include?("plastic-") }
+        end
+      end
+
+      if missing_events.empty?
+        checks << check(
+          category: "agent_registration", name: "hooks_registered", status: "pass",
+          message: "All #{CLAUDE_HOOK_EVENTS.size} hook events registered in settings.json"
+        )
+      else
+        checks << check(
+          category: "agent_registration", name: "hooks_registered", status: "fail",
+          message: "#{missing_events.size} hook event(s) not registered in settings.json",
+          details: missing_events,
+          fixable: true, fix_hint: "Re-run the Plastic installer: npx @zalom/plastic@latest --claude"
+        )
+      end
+
+      # hooks_match_registry (intent 108, D7): the live settings must carry
+      # EXACTLY the registrations HookRegistry defines; any drift (a missing
+      # gate, a stray plastic hook, a stale matcher) is how bash-gate shipped
+      # dead once already.
+      expected = HookRegistry.claude_settings_hooks(hook_dir: hooks_dir)
+      diffs = []
+      expected.each do |event, group|
+        groups = group.is_a?(Array) ? group : [group]
+        live = settings.dig("hooks", event) || []
+        groups.each do |g|
+          matches = live.select { |h| h.is_a?(Hash) && h["matcher"] == g["matcher"] }
+          wanted = g["hooks"].map { |h| h["command"] }
+          got = matches.flat_map { |m| Array(m["hooks"]).map { |h| h["command"] } }
+          missing = wanted - got
+          diffs << "#{event}[#{g['matcher']}] missing: #{missing.join(', ')}" unless missing.empty?
+        end
+      end
+      live_plastic = (settings["hooks"] || {}).flat_map do |event, groups|
+        Array(groups).flat_map do |g|
+          next [] unless g.is_a?(Hash) && g["hooks"].is_a?(Array)
+          g["hooks"].map { |h| h["command"].to_s }.select { |c| c.include?("plastic-") }
+                    .map { |c| "#{event}: #{c}" }
+        end
+      end
+      expected_cmds = expected.values.flat_map { |g| g.is_a?(Array) ? g : [g] }
+                              .flat_map { |g| g["hooks"].map { |h| h["command"] } }
+      strays = live_plastic.reject { |lp| expected_cmds.any? { |c| lp.end_with?(c) } }
+      diffs.concat(strays.map { |s| "stray: #{s}" })
+
+      checks << if diffs.empty?
+        check(category: "agent_registration", name: "hooks_match_registry",
+              status: "pass", message: "settings.json hooks match HookRegistry")
+      else
+        check(category: "agent_registration", name: "hooks_match_registry",
+              status: "fail", message: "#{diffs.size} hook registration(s) diverge from HookRegistry",
+              details: diffs, fixable: true,
+              fix_hint: "Re-run the installer merge: npx @zalom/plastic update (or ruby ~/.plastic/scripts/install.rb)")
+      end
+    end
+
+    # skills_exist — flat, hyphen-namespaced personal skills (plastic-<name>/)
+    checks << flat_skills_check(agent_dir, "--claude")
+
+    # stray_skills — installed plastic-* skill dir with no manifest entry (a leftover,
+    # e.g. an old-name copy after a rename; intent 158a AC15)
+    stray_check = stray_skills_check(agent_dir, "--claude", File.join(agent_dir, "plastic", "manifest.json"))
+    checks << stray_check if stray_check
+
+    # agents_exist — auto-mode role files (plastic-*.md) synced into <dir>/agents
+    checks << flat_agents_check(agent_dir, "--claude")
+
+    checks
+  end
+
+  def claude_dispatcher_gate_names(source)
+    case_start = source.index(/^\s*case gate\b/)
+    return nil unless case_start
+
+    case_body = source[case_start..-1]
+    end_idx = case_body.index(/^\s*end\b/)
+    scanned = end_idx ? case_body[0...end_idx] : case_body
+    names = scanned.scan(/^\s*when\s+"([^"]+)"/).flatten.uniq
+    names.empty? ? nil : names
+  end
+
+  def claude_hooks_implemented_check
+    dispatcher_path = File.join(plastic_home, "scripts", "hook-edit-gates")
+
+    unless File.exist?(dispatcher_path)
+      return check(
+        category: "agent_registration", name: "claude_hooks_implemented", status: "fail",
+        message: "scripts/hook-edit-gates not found at #{tilde(dispatcher_path)}; cannot verify " \
+                 "the edit-path gate registry and dispatcher agree",
+        fixable: true, fix_hint: "Re-run the Plastic installer"
+      )
+    end
+
+    dispatcher_names = claude_dispatcher_gate_names(File.read(dispatcher_path))
+
+    if dispatcher_names.nil?
+      return check(
+        category: "agent_registration", name: "claude_hooks_implemented", status: "fail",
+        message: "Could not read any gate names out of #{tilde(dispatcher_path)}: the `case gate` " \
+                 "statement no longer matches the shape this check expects, so the registry was " \
+                 "never actually checked against the real dispatcher. Update " \
+                 "claude_dispatcher_gate_names in doctor.rb to the file's new shape.",
+        fixable: false
+      )
+    end
+
+    registry_names = HookRegistry::GATE_TOOLS.keys
+    missing_branch = registry_names - dispatcher_names
+    dead_branch = dispatcher_names - registry_names
+
+    if missing_branch.empty? && dead_branch.empty?
+      return check(
+        category: "agent_registration", name: "claude_hooks_implemented", status: "pass",
+        message: "Every registered edit-path gate has a scripts/hook-edit-gates branch, and every " \
+                 "dispatcher branch is registered"
+      )
+    end
+
+    details = missing_branch.map do |name|
+      "#{name} is in HookRegistry::GATE_TOOLS but scripts/hook-edit-gates has no branch for it, " \
+        "so the dispatcher skips it on every edit and it never blocks anything"
+    end
+    details += dead_branch.map do |name|
+      "#{name} has a branch in scripts/hook-edit-gates but is not in HookRegistry::GATE_TOOLS, so " \
+        "the dispatcher never reaches it and it is dead code"
+    end
+
+    check(
+      category: "agent_registration", name: "claude_hooks_implemented", status: "fail",
+      message: "The edit-path gate registry and scripts/hook-edit-gates disagree on " \
+               "#{details.size} gate(s)",
+      details: details, fixable: false
+    )
+  end
+
+  def flat_skills_check(agent_dir, installer_flag)
+    skills_root = File.join(agent_dir, "skills")
+    found = Dir.glob(File.join(skills_root, "plastic-*", "SKILL.md"))
+
+    if !found.empty?
+      check(
+        category: "agent_registration", name: "skills_exist", status: "pass",
+        message: "#{found.size} plastic-* skill(s) installed in #{tilde(skills_root)}"
+      )
+    else
+      check(
+        category: "agent_registration", name: "skills_exist", status: "fail",
+        message: "No plastic-* skills found in #{tilde(skills_root)}",
+        fixable: true, fix_hint: "Re-run the Plastic installer: npx @zalom/plastic@latest #{installer_flag}"
+      )
+    end
+  end
+
+  def stray_skills_check(agent_dir, installer_flag, manifest_path)
+    skills_root = File.join(agent_dir, "skills")
+    manifest = read_json_safe(manifest_path)
+    files = manifest.is_a?(Hash) ? manifest["files"] : nil
+    return nil unless files.is_a?(Hash)
+
+    installed = Dir.glob(File.join(skills_root, "plastic-*", "SKILL.md"))
+                    .map { |f| File.basename(File.dirname(f)) }
+    tracked = files.keys
+                   .select { |p| p.start_with?("#{skills_root}/") }
+                   .map { |p| p.sub("#{skills_root}/", "").split("/").first }
+                   .uniq
+
+    strays = (installed - tracked).sort
+
+    if strays.empty?
+      check(
+        category: "agent_registration", name: "stray_skills", status: "pass",
+        message: "No stray plastic-* skill directories in #{tilde(skills_root)}"
+      )
+    else
+      check(
+        category: "agent_registration", name: "stray_skills", status: "warn",
+        message: "#{strays.size} installed skill dir(s) not in the current manifest (stray, e.g. a leftover old-name copy)",
+        details: strays,
+        fixable: true, fix_hint: "Re-run the Plastic installer: npx @zalom/plastic@latest #{installer_flag}"
+      )
+    end
+  end
+
+  def flat_agents_check(agent_dir, installer_flag)
+    agents_root = File.join(agent_dir, "agents")
+    found = Dir.glob(File.join(agents_root, "plastic-*.md"))
+
+    if !found.empty?
+      check(
+        category: "agent_registration", name: "agents_exist", status: "pass",
+        message: "#{found.size} plastic-* agent(s) installed in #{tilde(agents_root)}"
+      )
+    else
+      check(
+        category: "agent_registration", name: "agents_exist", status: "fail",
+        message: "No plastic-* agents found in #{tilde(agents_root)}",
+        fixable: true, fix_hint: "Re-run the Plastic installer: npx @zalom/plastic@latest #{installer_flag}"
+      )
+    end
+  end
+
+  def check_flat_skills_and_stray(agent_key, agent_dir)
+    checks = []
+
+    # For codex/hermes: just check skills exist (no settings.json hooks)
+    checks << flat_skills_check(agent_dir, "--#{agent_key}")
+
+    # stray_skills — installed plastic-* skill dir with no manifest entry (a leftover,
+    # e.g. an old-name copy after a rename; intent 158a AC15)
+    stray_check = stray_skills_check(agent_dir, "--#{agent_key}", File.join(agent_dir, "plastic", "manifest.json"))
+    checks << stray_check if stray_check
+
+    checks
+  end
+
+  def check_generic_agent_registration(agent_key, agent_dir)
+    checks = check_flat_skills_and_stray(agent_key, agent_dir)
+    checks << flat_agents_check(agent_dir, "--#{agent_key}")   # hermes: unchanged (.md copy)
+    checks
+  end
+
+  # Codex marker literals. Keep in sync with InstallerCore::CODEX_SECTION_BEGIN_PREFIX /
+  # CODEX_SECTION_END (doctor does not require installer_core, so the literals are duplicated).
+  CODEX_SECTION_BEGIN_PREFIX = "<!-- BEGIN PLASTIC INTEGRATION"
+  CODEX_SECTION_END = "<!-- END PLASTIC INTEGRATION -->"
+
+  def check_codex_registration(agent_key, agent_dir)
+    config = agents[agent_key]
+    checks = check_flat_skills_and_stray(agent_key, agent_dir)
+    checks << codex_agents_toml_check(config)
+
+    agents_md = File.join(config[:home_dir], "AGENTS.md")
+
+    if !File.exist?(agents_md)
+      checks << check(
+        category: "agent_registration", name: "codex_agents_md", status: "fail",
+        message: "Codex AGENTS.md not found at #{tilde(agents_md)}",
+        fixable: true, fix_hint: "Re-run the Plastic installer with --codex"
+      )
+    else
+      content = File.read(agents_md)
+      b = content.index(CODEX_SECTION_BEGIN_PREFIX)
+      e = content.index(CODEX_SECTION_END)
+      well_formed = b && e && e > b && content[b...e].include?("-->")
+      if well_formed
+        checks << check(
+          category: "agent_registration", name: "codex_agents_md", status: "pass",
+          message: "Codex AGENTS.md carries the Plastic section"
+        )
+      else
+        checks << check(
+          category: "agent_registration", name: "codex_agents_md", status: "fail",
+          message: "Codex AGENTS.md is missing or has a malformed Plastic section",
+          fixable: true, fix_hint: "Re-run the Plastic installer with --codex"
+        )
+      end
+    end
+
+    hooks_check = codex_hooks_registered_check(config)
+    checks << hooks_check
+    checks << codex_hooks_implemented_check(config)
+    checks << codex_hook_trust_advisory_check if hooks_check[:status] == "pass"
+    codex_config_toml_advisory_check(config).tap { |c| checks << c if c }
+    codex_version_floor_check(config).tap { |c| checks << c if c }
+
+    checks
+  end
+
+  # Hooks being REGISTERED (hooks.json content matches HookRegistry) is not
+  # the same as hooks being TRUSTED: Codex gates every non-managed hook
+  # command behind a human /hooks review, keyed by the command's current
+  # hash, so a release that changes a hook command re-arms the review
+  # (intent 198, Decision D2). Whether Codex persists a queryable trust
+  # record anywhere under ~/.codex is undocumented and unverified, so this
+  # can never be a real pass or fail on trust state; it is an advisory that
+  # always names the /hooks step, and it fires only once hooks are actually
+  # registered (an unregistered hook is already reported by
+  # codex_hooks_registered_check, so reminding about trust on top of that
+  # would be noise, not signal).
+  def codex_hook_trust_advisory_check
+    check(
+      category: "agent_registration", name: "codex_hooks_trust", status: "warn",
+      message: "Open Codex, run /hooks, and trust the Plastic hook definitions. " \
+               "Codex re-arms this review whenever a hook's command changes.",
+      fixable: false
+    )
+  end
+
+  # Codex-specific agent presence + structural sanity: ~/.codex/agents/plastic-*.toml
+  # exist and each carries the mandatory fields. No TOML parser (doctor depends on none):
+  # "structural" means the mandatory keys appear as lines and the multi-line
+  # developer_instructions string is balanced (an opening triple-quote has a later one).
+  def codex_agents_toml_check(config)
+    agents_root = File.join(config[:home_dir], "agents")
+    found = Dir.glob(File.join(agents_root, "plastic-*.toml"))
+
+    if found.empty?
+      return check(
+        category: "agent_registration", name: "codex_agents_toml", status: "fail",
+        message: "No plastic-* agent TOML files found in #{tilde(agents_root)}",
+        fixable: true, fix_hint: "Re-run the Plastic installer with --codex"
+      )
+    end
+
+    malformed = found.reject { |f| codex_agent_toml_well_formed?(File.read(f)) }
+    if malformed.empty?
+      check(
+        category: "agent_registration", name: "codex_agents_toml", status: "pass",
+        message: "#{found.size} plastic-* agent TOML(s) installed in #{tilde(agents_root)}"
+      )
+    else
+      check(
+        category: "agent_registration", name: "codex_agents_toml", status: "fail",
+        message: "#{malformed.size} Codex agent TOML(s) missing mandatory fields",
+        details: malformed.map { |f| tilde(f) },
+        fixable: true, fix_hint: "Re-run the Plastic installer with --codex"
+      )
+    end
+  end
+
+  def codex_agent_toml_well_formed?(content)
+    marker = 'developer_instructions = """'
+    di = content.index(marker)
+    has_name = content.match?(/^name\s*=\s*"/)
+    has_desc = content.match?(/^description\s*=\s*"/)
+    balanced = di && content.index('"""', di + marker.length)
+    has_name && has_desc && !di.nil? && !balanced.nil?
+  end
+
+  def codex_hooks_registered_check(config)
+    hooks_json = File.join(config[:home_dir], "hooks.json")
+    dispatcher = File.join(plastic_home, "scripts", "codex-hook")
+    data = read_json_safe(hooks_json)
+
+    if data.nil?
+      return check(
+        category: "agent_registration", name: "codex_hooks_registered", status: "fail",
+        message: "Codex hooks.json missing or unreadable at #{tilde(hooks_json)}",
+        fixable: true, fix_hint: "Re-run the Plastic installer with --codex"
+      )
+    end
+
+    expected = HookRegistry.codex_hooks_json(dispatcher_path: dispatcher)
+    live = data["hooks"] || {}
+    missing = []
+    expected.each do |event, groups|
+      want = Array(groups).flat_map { |g| g["hooks"].map { |h| h["command"] } }
+      got = Array(live[event]).flat_map { |g| Array(g["hooks"]).map { |h| h["command"] } }
+      missing.concat(want - got)
+    end
+
+    if missing.empty?
+      check(
+        category: "agent_registration", name: "codex_hooks_registered", status: "pass",
+        message: "Codex hooks registered in hooks.json"
+      )
+    else
+      check(
+        category: "agent_registration", name: "codex_hooks_registered", status: "fail",
+        message: "Codex hooks.json missing #{missing.size} command(s)",
+        details: missing,
+        fixable: true, fix_hint: "Re-run the Plastic installer with --codex"
+      )
+    end
+  end
+
+  # codex_hooks_implemented (intent 200): codex_hooks_registered_check above proves
+  # hooks.json content matches what HookRegistry would emit; both sides of THAT
+  # comparison come from the registry, so a pass only proves the registry agrees
+  # with itself. It never looks at the actual dispatcher, so it cannot see a
+  # registered gate with no real branch there (links-gate shipped exactly this way,
+  # dead, in v1.4.0/intent 192, invisible to doctor and the suite until 198 found it
+  # by hand), or a dispatcher branch nobody registers (bash-gate's shape, intent
+  # 203, in the opposite direction). This check closes both directions at once.
+
+  # The Codex gate names HookRegistry actually registers: the six apply_patch-gated
+  # names (CODEX_PRE_HOOKS + CODEX_POST_HOOKS), the two Bash-matcher shell gates
+  # (CODEX_BASH_HOOKS), and the live-state hook names Codex inherits whole from
+  # `events` (CODEX_LIVE_STATE_EVENTS). No parsing needed: these are HookRegistry's
+  # own Ruby constants.
+  def codex_registry_gate_names
+    live_state = HookRegistry::CODEX_LIVE_STATE_EVENTS.flat_map do |event|
+      HookRegistry.events[event].flat_map { |g| g["hooks"].map { |h| h["name"] } }
+    end
+    (HookRegistry::CODEX_PRE_HOOKS + HookRegistry::CODEX_POST_HOOKS +
+     HookRegistry::CODEX_BASH_HOOKS + live_state).uniq
+  end
+
+  def codex_dispatcher_gate_names(source)
+    names = []
+    %w[STATE_HOOKS SHELL_HOOKS].each do |const|
+      m = source.match(/^#{const}\s*=\s*%w\[([^\]]*)\]/)
+      names.concat(m[1].split(/\s+/)) if m
+    end
+
+    case_start = source.index(/^case gate\b/)
+    if case_start
+      case_body = source[case_start..-1]
+      else_idx = case_body.index(/^else\b/)
+      scanned = else_idx ? case_body[0...else_idx] : case_body
+      names.concat(scanned.scan(/^when\s+"([^"]+)"/).flatten)
+    end
+
+    names.uniq!
+    names.empty? ? nil : names
+  end
+
+  # The both-direction diff. Each mismatch becomes one detail line naming the
+  # hook, the direction, the harness ("Codex"), and the concrete runtime effect,
+  # never a generic "Codex hooks drift" message (D4).
+  def codex_hooks_implemented_check(config)
+    dispatcher_path = File.join(plastic_home, "scripts", "codex-hook")
+
+    unless File.exist?(dispatcher_path)
+      return check(
+        category: "agent_registration", name: "codex_hooks_implemented", status: "fail",
+        message: "scripts/codex-hook not found at #{tilde(dispatcher_path)}; cannot verify " \
+                 "the Codex hook registry and dispatcher agree",
+        fixable: true, fix_hint: "Re-run the Plastic installer with --codex"
+      )
+    end
+
+    dispatcher_names = codex_dispatcher_gate_names(File.read(dispatcher_path))
+
+    if dispatcher_names.nil?
+      return check(
+        category: "agent_registration", name: "codex_hooks_implemented", status: "fail",
+        message: "Could not read any gate names out of #{tilde(dispatcher_path)}: the " \
+                 "STATE_HOOKS/SHELL_HOOKS constants and the `case gate` statement no longer " \
+                 "match the shape this check expects, so the registry could not be checked " \
+                 "against the real dispatcher. This is exactly the silent-pass failure this " \
+                 "check exists to prevent; update codex_dispatcher_gate_names in doctor.rb " \
+                 "to the file's new shape.",
+        fixable: false
+      )
+    end
+
+    registry_names = codex_registry_gate_names
+    missing_dispatcher_branch = registry_names - dispatcher_names
+    dead_branch = dispatcher_names - registry_names
+
+    if missing_dispatcher_branch.empty? && dead_branch.empty?
+      return check(
+        category: "agent_registration", name: "codex_hooks_implemented", status: "pass",
+        message: "Every Codex-registered gate has a scripts/codex-hook branch, and every " \
+                 "dispatcher branch is registered"
+      )
+    end
+
+    details = missing_dispatcher_branch.map do |name|
+      "#{name} is registered in ~/.codex/hooks.json but scripts/codex-hook has no branch " \
+        "for it, so it always falls through to the fail-open else and always allows the write"
+    end
+    details += dead_branch.map do |name|
+      "#{name} has a branch in scripts/codex-hook but is not registered in HookRegistry for " \
+        "Codex, so it is dead code Codex never reaches"
+    end
+
+    check(
+      category: "agent_registration", name: "codex_hooks_implemented", status: "fail",
+      message: "Codex's hook registry and scripts/codex-hook disagree on #{details.size} gate(s)",
+      details: details,
+      fixable: false
+    )
+  end
+
+  def codex_config_toml_advisory_check(config)
+    config_toml = File.join(config[:home_dir], "config.toml")
+    return nil unless File.exist?(config_toml)
+
+    toml = File.read(config_toml) rescue ""
+    warns = []
+    # guide Part 3: `codex_hooks` is a deprecated alias for `[features] hooks`; catch both.
+    warns << "hooks are disabled ([features] hooks = false); Plastic gates will not fire" if toml.match?(/^\s*(?:codex_)?hooks\s*=\s*false/)
+    warns << "sandbox_mode = \"read-only\"; apply_patch writes (and gates) cannot run" if toml.match?(/^\s*sandbox_mode\s*=\s*["']read-only["']/)
+    return nil if warns.empty?
+
+    check(
+      category: "agent_registration", name: "codex_config_advisory", status: "warn",
+      message: warns.join("; "),
+      fixable: false,
+      fix_hint: "Set [features] hooks = true and sandbox_mode = \"workspace-write\" in ~/.codex/config.toml"
+    )
+  end
+
+  # Codex version-floor advisory (intent 184): READ ONLY. The apply_patch PreToolUse
+  # veto (scripts/lib/hook_registry.rb, scripts/codex-hook) only fires from Codex
+  # v0.123.0 (PR #18391); below it the veto silently no-ops. version.json is Codex's
+  # update-checker cache and holds no installed version, so the only install-method-
+  # agnostic source is `codex --version`, shelled out through the injected runner.
+  # Four honest branches (intent 208, no pass-by-construction): absent home -> nil;
+  # present but undetectable -> distinct warn; below floor -> warn; at/above -> pass.
+  def codex_version_floor_check(config)
+    return nil unless File.exist?(config[:home_dir])
+
+    stdout, ok = @runner.call(["--version"])
+    version = ok ? codex_version_from_output(stdout) : nil
+    parsed = version && safe_version(version)
+
+    if parsed.nil?
+      return check(
+        category: "agent_registration", name: "codex_version_floor", status: "warn",
+        message: "Could not determine the installed Codex version (`codex --version` did not " \
+                 "return a parseable version); Plastic cannot confirm the apply_patch hooks " \
+                 "floor v#{CODEX_HOOKS_FLOOR} is met, so its gate may silently no-op",
+        fixable: false,
+        fix_hint: "Ensure `codex` is on PATH and `codex --version` >= #{CODEX_HOOKS_FLOOR}"
+      )
+    end
+
+    if parsed < safe_version(CODEX_HOOKS_FLOOR)
+      return check(
+        category: "agent_registration", name: "codex_version_floor", status: "warn",
+        message: "Installed Codex #{version} predates v#{CODEX_HOOKS_FLOOR}; the apply_patch " \
+                 "PreToolUse veto only exists from v#{CODEX_HOOKS_FLOOR} (PR #18391), so Plastic's " \
+                 "gate silently no-ops on this install",
+        fixable: false,
+        fix_hint: "Upgrade Codex to v#{CODEX_HOOKS_FLOOR} or newer with your install method " \
+                  "(npm i -g @openai/codex, mise, homebrew, or cargo)"
+      )
+    end
+
+    check(
+      category: "agent_registration", name: "codex_version_floor", status: "pass",
+      message: "Codex #{version} meets the apply_patch hooks floor v#{CODEX_HOOKS_FLOOR}"
+    )
+  end
+
+  def codex_version_from_output(stdout)
+    m = stdout.to_s.match(/(\d+\.\d+\.\d+(?:[.\-+][0-9A-Za-z.\-+]*)?)/)
+    m && m[1]
+  end
+
+  def safe_version(str)
+    Gem::Version.new(str.to_s)
+  rescue ArgumentError
+    nil
+  end
+
+  def check_core_files(agent_key, include_drift: true)
+    checks = []
+
+    # plastic_md
+    plastic_md = File.join(plastic_home, "PLASTIC.md")
+    if File.exist?(plastic_md)
+      checks << check(
+        category: "core_files", name: "plastic_md", status: "pass",
+        message: "PLASTIC.md exists"
+      )
+    else
+      checks << check(
+        category: "core_files", name: "plastic_md", status: "fail",
+        message: "PLASTIC.md not found at #{tilde(plastic_md)}",
+        fixable: true, fix_hint: "Re-run the Plastic installer to restore core files"
+      )
+    end
+
+    # version_file
+    version_path = File.join(plastic_home, "VERSION")
+    if File.exist?(version_path)
+      checks << check(
+        category: "core_files", name: "version_file", status: "pass",
+        message: "VERSION file exists"
+      )
+    else
+      checks << check(
+        category: "core_files", name: "version_file", status: "fail",
+        message: "VERSION file not found at #{tilde(version_path)}",
+        fixable: true, fix_hint: "Re-run the Plastic installer to restore core files"
+      )
+    end
+
+    # scripts_present
+    scripts_dir = File.join(plastic_home, "scripts")
+    missing_scripts = REQUIRED_SCRIPTS.reject { |s| File.exist?(File.join(scripts_dir, s)) }
+
+    if missing_scripts.empty?
+      checks << check(
+        category: "core_files", name: "scripts_present", status: "pass",
+        message: "All #{REQUIRED_SCRIPTS.size} required scripts present"
+      )
+    else
+      checks << check(
+        category: "core_files", name: "scripts_present", status: "fail",
+        message: "#{missing_scripts.size} required script(s) missing from #{tilde(scripts_dir)}",
+        details: missing_scripts,
+        fixable: true, fix_hint: "Re-run the Plastic installer to restore scripts"
+      )
+    end
+
+    # scripts_executable
+    if File.directory?(scripts_dir)
+      script_files = Dir.children(scripts_dir)
+        .map { |f| File.join(scripts_dir, f) }
+        .select { |f| File.file?(f) }
+
+      non_executable = script_files.reject { |f| File.executable?(f) }
+
+      if non_executable.empty?
+        checks << check(
+          category: "core_files", name: "scripts_executable", status: "pass",
+          message: "All scripts in #{tilde(scripts_dir)} are executable"
+        )
+      else
+        checks << check(
+          category: "core_files", name: "scripts_executable", status: "fail",
+          message: "#{non_executable.size} script(s) not executable",
+          details: non_executable.map { |f| tilde(f) },
+          fixable: true, fix_hint: "chmod +x on the listed files"
+        )
+      end
+    end
+
+    # version_match — compare global VERSION with agent-side VERSION
+    global_version = read_version
+    agent_config = agents[agent_key]
+
+    if global_version && agent_config
+      agent_version_path = case agent_key
+                           when "claude" then File.join(agent_config[:dir], "plastic", "VERSION")
+                           else File.join(agent_config[:dir], "plastic", "VERSION")
+                           end
+
+      if File.exist?(agent_version_path)
+        agent_version = File.read(agent_version_path).strip
+
+        if global_version == agent_version
+          checks << check(
+            category: "core_files", name: "version_match", status: "pass",
+            message: "Global VERSION (#{global_version}) matches agent-side VERSION"
+          )
+        else
+          checks << check(
+            category: "core_files", name: "version_match", status: "warn",
+            message: "Version mismatch: global=#{global_version}, agent=#{agent_version}",
+            details: [
+              "#{tilde(File.join(plastic_home, "VERSION"))}: #{global_version}",
+              "#{tilde(agent_version_path)}: #{agent_version}",
+            ],
+            fixable: true,
+            fix_hint: "Re-sync the stale harness: npx @zalom/plastic@latest install --reinstall <flag>, or plastic-rollback to a prior version"
+          )
+        end
+      else
+        checks << check(
+          category: "core_files", name: "version_match", status: "warn",
+          message: "Agent-side VERSION file not found at #{tilde(agent_version_path)}",
+          fixable: true,
+          fix_hint: "Re-sync the stale harness: npx @zalom/plastic@latest install --reinstall <flag>, or plastic-rollback to a prior version"
+        )
+      end
+    end
+
+    checks += check_agent_model_drift(agent_key) if include_drift
+
+    checks
+  end
+
+  def check_manifest_sync(agent_key)
+    checks = []
+
+    global_manifest = File.join(plastic_home, "manifest.json")
+    checks << verify_manifest(global_manifest, "global")
+
+    agent_dir = agents[agent_key][:dir]
+    agent_manifest = File.join(agent_dir, "plastic", "manifest.json")
+    checks << verify_manifest(agent_manifest, "agent")
+
+    checks
+  end
+
+  # Check one manifest file. Returns a single check (pass or fail).
+  def verify_manifest(manifest_path, label)
+    unless File.exist?(manifest_path)
+      return check(
+        category: "manifest_sync", name: "#{label}_manifest", status: "fail",
+        message: "#{label} core manifest missing — re-run the Plastic installer",
+        details: [tilde(manifest_path)],
+        fixable: true, fix_hint: "Re-run the Plastic installer"
+      )
+    end
+
+    data = read_json_safe(manifest_path)
+    files = data.is_a?(Hash) ? data["files"] : nil
+    unless files.is_a?(Hash)
+      return check(
+        category: "manifest_sync", name: "#{label}_manifest", status: "fail",
+        message: "#{label} core manifest unreadable or malformed — re-run the Plastic installer",
+        details: [tilde(manifest_path)],
+        fixable: true, fix_hint: "Re-run the Plastic installer"
+      )
+    end
+
+    missing = []
+    mismatched = []
+    files.each do |path, recorded|
+      unless File.exist?(path)
+        missing << tilde(path)
+        next
+      end
+      actual = Digest::SHA256.file(path).hexdigest
+      mismatched << tilde(path) if actual != recorded
+    end
+
+    if missing.empty? && mismatched.empty?
+      check(
+        category: "manifest_sync", name: "#{label}_manifest", status: "pass",
+        message: "#{label} manifest: all #{files.size} tracked file(s) present and matching"
+      )
+    else
+      details = []
+      details += missing.map { |p| "missing: #{p}" }
+      details += mismatched.map { |p| "modified: #{p}" }
+      check(
+        category: "manifest_sync", name: "#{label}_manifest", status: "fail",
+        message: "#{label} manifest out of sync: #{missing.size} missing, #{mismatched.size} modified",
+        details: details,
+        fixable: true, fix_hint: "Re-run the Plastic installer to restore tracked files"
+      )
+    end
+  end
+
+
+  # Binary core sync check: agent registration + core files (drift excluded) + manifest
+  # sync + registered project paths + global store availability, rolled up with binary:
+  # true so ANY warn or fail makes the overall status "fail" (and "warn" is never
+  # emitted). Used by `doctor.rb --core` (219 D1/D2: operational readiness only, no
+  # agent_model_drift, no store-content scanning).
+  def run_core_checks(agent_key)
+    all_checks = []
+    all_checks += check_agent_registration(agent_key)
+    all_checks += check_core_files(agent_key, include_drift: false)
+    all_checks += check_manifest_sync(agent_key)
+    all_checks += check_registered_project_paths
+    all_checks += check_global_store_available
+
+    summarize(all_checks, agent_key, binary: true)
+  end
+
+  def check_registered_project_paths
+    checks = []
+
+    projects_yml_path = File.join(plastic_home, "projects.yml")
+    projects_data = load_yaml_safe(projects_yml_path)
+
+    if projects_data.nil?
+      checks << check(
+        category: "project_stores", name: "registered_project_paths", status: "fail",
+        message: "projects.yml not found or invalid at #{tilde(projects_yml_path)}",
+        fixable: true, fix_hint: "Re-run the Plastic installer to restore projects.yml"
+      )
+      return checks
+    end
+
+    projects = projects_data["projects"]
+    unless projects.is_a?(Hash) && !projects.empty?
+      checks << check(
+        category: "project_stores", name: "registered_project_paths", status: "pass",
+        message: "No projects registered"
+      )
+      return checks
+    end
+
+    projects.each do |slug, project_info|
+      path = project_info.is_a?(Hash) ? project_info["path"] : nil
+
+      if path && File.directory?(path)
+        checks << check(
+          category: "project_stores", name: "project_path_resolves", status: "pass",
+          message: "Registered path for '#{slug}' resolves to a real directory"
+        )
+      else
+        checks << check(
+          category: "project_stores", name: "project_path_resolves", status: "fail",
+          message: "Registered path for '#{slug}' does not resolve to a real directory",
+          details: [path ? tilde(path) : "(no path set in projects.yml)"],
+          fixable: false
+        )
+      end
+    end
+
+    checks
+  end
+
+  # Roll a list of checks up into the standard result envelope.
+  # When binary: true, the overall status is "pass" only if there are zero warn
+  # AND zero fail; any warn or fail yields "fail" (never "warn"). When false
+  # (the default) the classic 3-state pass/warn/fail roll-up is used.
+  def summarize(all_checks, agent_key, binary: false)
+    summary = { pass: 0, warn: 0, fail: 0, total: all_checks.size }
+    all_checks.each { |c| summary[c[:status].to_sym] += 1 }
+
+    overall = if binary
+                (summary[:fail] > 0 || summary[:warn] > 0) ? "fail" : "pass"
+              elsif summary[:fail] > 0
+                "fail"
+              elsif summary[:warn] > 0
+                "warn"
+              else
+                "pass"
+              end
+
+    {
+      version: read_version || "unknown",
+      timestamp: Time.now.utc.strftime("%Y-%m-%dT%H:%M:%SZ"),
+      status: overall,
+      agent: agent_key,
+      checks: all_checks,
+      summary: summary,
+    }
+  end
+end