@zalom/plastic 1.8.0 → 1.10.0

package/scripts/doctor.rb

@@ -9,12 +9,9 @@
 # Exit codes: 0 (all pass), 1 (warnings only), 2 (failures present)
 # Read-only — never modifies files.
 
-require "json"
-require "yaml"
-require "time"
 require "date"
-require "digest"
-require "rubygems"
+
+require_relative "lib/doctor_core"
 
 require_relative "lib/qmd_sync"
 require_relative "lib/intent_validator"
@@ -22,7 +19,6 @@ require_relative "lib/graph_rebuild"
 require_relative "lib/store_discovery"
 require_relative "lib/links_projection"
 require_relative "lib/links_section"
-require_relative "lib/hook_registry"
 require_relative "lib/lock"
 require_relative "lib/bridge"
 require_relative "lib/agent_models"
@@ -30,18 +26,16 @@ require_relative "lib/outcome_guard"
 require_relative "lib/skill_lint"
 require_relative "lib/config_asks"
 require_relative "lib/power_tools"
+require_relative "lib/preflight"
+require_relative "lib/ruby_probe"
 
 # Diagnostic engine, instantiable with an injected store/agent map so tests can
 # run it hermetically (no eval, no global-constant rewriting).
+# Reopens the core class defined in lib/doctor_core.rb (intent 228): that file
+# holds run_core_checks and its transitive dependencies, this file adds the
+# store, conventions, intent and CLI halves, so Doctor stays one class with one
+# public surface.
 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
 
   REQUIRED_INDEX_SECTIONS = ["## Active", "## Future", "## Clusters", "## Abandoned", "## Completed"].freeze
 
@@ -49,51 +43,7 @@ class Doctor
   # (intent 60). Alias it here so the two can never drift.
   REQUIRED_FRONTMATTER_FIELDS = IntentValidator::REQUIRED_FIELDS
 
-  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
 
   # --- Flag parsing ---
 
@@ -180,51 +130,6 @@ class Doctor
     HELP
   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
 
   # --- Parse frontmatter from an intent markdown file ---
 
@@ -379,39 +284,6 @@ class Doctor
   # Narrow, core-appropriate version of check_global_store: presence/readability only, zero
   # content scanning. check_global_store (above) is store/full-scope and includes
   # orphaned_intents / ghost_references, both explicitly forbidden at core by D1.
-  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
 
   # --- Check category 2: Conventions ---
 
@@ -560,7 +432,7 @@ class Doctor
         fixable: true,
         fix_hint: "Dispatch plastic-store-curating to relocate each unsanctioned section into the " \
                   "intent's revisions.md via move-and-record (a missing required section is restored " \
-                  "or reprojected instead); see PLASTIC.md > Structural maintenance and revisions.md"
+                  "or reprojected instead); see plastic-conventions > references/maintenance-and-revisions.md"
       )
     end
 
@@ -929,7 +801,7 @@ end
       "project-links --intent <id> --apply` over running project-links directly: it detects " \
       "(never acquires) the target's delivery lock, requires a clean store working tree, and " \
       "commits the scoped change plus its revisions.md receipt as one merged operation " \
-      "(PLASTIC.md > WORK vs MAINTENANCE)."
+      "(plastic-conventions > references/maintenance-and-revisions.md)."
     )
   end
 
@@ -1229,7 +1101,7 @@ end
       "Every sources/chain id resolves to a real intent (I4)",
       "Dispatch plastic-store-curating to record the dangling sources/chain edge as a " \
       "broken-source/broken-chain move-and-record entry in the intent's revisions.md (see " \
-      "PLASTIC.md > Structural maintenance and revisions.md), or restore the missing intent"
+      "plastic-conventions > references/maintenance-and-revisions.md), or restore the missing intent"
     )
     checks
   end
@@ -1252,210 +1124,22 @@ end
 
   # --- Check category 3: Agent registration ---
 
-  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
-
-    # 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
+  # claude_hooks_implemented (intent 244, the Claude twin of intent 200's Codex
+  # check): the edit-path gates now live as branches inside one dispatcher,
+  # which is exactly the shape that let links-gate ship registered and dead on
+  # Codex. HookRegistry::GATE_TOOLS is the registry side; scripts/hook-edit-gates
+  # is the implementation side. Checked in BOTH directions, so a registered gate
+  # with no branch (always allows, silently) and a branch nobody registers
+  # (dead code) are both reported.
+  #
+  # Read as plain text, never required: the dispatcher has top-level side effects
+  # (it reads $stdin and exits), the same reason codex_dispatcher_gate_names reads
+  # scripts/codex-hook as text.
 
   # Plastic skills install as ~/.claude/skills/plastic-<name>/SKILL.md. Pass if at
   # least one such skill is present.
-  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
 
   # Backstop for a rename or removal (intent 158a, AC15): an installed plastic-*
   # skill directory under agent_dir/skills that has NO corresponding entry in the
@@ -1464,258 +1148,39 @@ end
   # manifest predates it). Complements flat_skills_check (which only confirms at
   # least one skill exists). Defers to the manifest check when the manifest itself
   # is missing or malformed, so the two checks never double-report the same gap.
-  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
 
   # Auto-mode role agents install as <dir>/agents/plastic-*.md. Pass if at least
   # one such role file is present (the installer syncs agents/ on every install).
-  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
 
   # Shared skills-presence plus stray-skills check, used by both the generic
   # (hermes) agent-registration path and codex's TOML-based one. Neither the flat
   # `.md` agents check nor anything agent-format-specific lives here.
-  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
-
-  # Plain string extraction of the single model-selection line a generated
-  # Codex agent TOML carries (model_reasoning_effort for a tier alias, model
-  # for a literal override id; codex_model_fields never emits both). No TOML
-  # parser dependency, mirroring codex_agent_toml_well_formed? above.
-  def codex_agent_toml_model_value(content)
-    m = content.match(/^model_reasoning_effort\s*=\s*"([^"]*)"/) || content.match(/^model\s*=\s*"([^"]*)"/)
-    m && m[1]
+  # Plain string extraction of the two model-selection lines a generated
+  # Codex agent TOML can carry, read separately (intent 216). Per the
+  # emission contract in installer_core.rb's codex_model_fields: a tier
+  # alias emits BOTH `model` and `model_reasoning_effort` (model first); a
+  # literal Codex model id override emits `model` only, no effort line; an
+  # empty value emits neither. No TOML parser dependency, mirroring
+  # codex_agent_toml_well_formed? above.
+  #
+  # Regex detail: `/^model\s*=\s*"([^"]*)"/` cannot match a
+  # `model_reasoning_effort = "..."` line, because the character right
+  # after `model` there is `_`, which matches neither `\s` nor `=`. The two
+  # matchers are independent lookups and need no ordering trick, unlike the
+  # single-value extractor this replaces. `^` anchors at line start in
+  # Ruby by default, so no `/m` flag is needed.
+  def codex_agent_toml_model_fields(content)
+    model = content.match(/^model\s*=\s*"([^"]*)"/)
+    effort = content.match(/^model_reasoning_effort\s*=\s*"([^"]*)"/)
+    { model: model && model[1], effort: effort && effort[1] }
   end
 
   # codex_hooks_registered (intent 102, the owner-facing first-run validation
   # path, Decision 14): ~/.codex/hooks.json must carry EXACTLY the commands
   # HookRegistry.codex_hooks_json defines, mirroring the Claude
   # hooks_match_registry diff. Never writes.
-  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
 
   # Source-text extraction of scripts/codex-hook's supported gate names (D3): the
   # dispatcher is an executable script with real top-level side effects (it reads
@@ -1735,280 +1200,13 @@ end
   # finds nothing and calls that healthy IS the exact disease this whole check
   # exists to catch, one level up, so nil forces the caller (below) to fail loudly
   # instead of reporting health it never actually verified.
-  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
 
   # config.toml advisory (intent 102, Decision 2, R2): READ ONLY. Warns on the two
   # documented footguns (hooks disabled, sandbox read-only); never writes, and
   # returns nil (no check emitted) when config.toml is absent or carries neither.
-  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
 
   # --- Check category 4: Core files ---
 
-  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
 
   # agent_model_drift - advisory (never fail) config-vs-frontmatter comparison
   # for every installed <agent_dir>/agents/plastic-*.md file (intent 170, D1;
@@ -2123,18 +1321,39 @@ end
     end
   end
 
-  # Codex leg of agent_model_drift (intent 198, Decision D4): the shared .md
-  # path above is structurally blind on Codex (codex agents are TOML under
-  # ~/.codex/agents/, never ~/.agents/agents/*.md), so it always passed on an
-  # empty glob without opening a single Codex file. This mirrors the same
-  # four buckets (sanctioned override, matches default, drifted,
-  # unclassified) against ~/.codex/agents/plastic-*.toml instead, reading
-  # model / model_reasoning_effort with the same plain string matching
+  # Codex leg of agent_model_drift (intent 198, Decision D4; widened intent
+  # 216 to cover both TOML lines). The shared .md path above is structurally
+  # blind on Codex (codex agents are TOML under ~/.codex/agents/, never
+  # ~/.agents/agents/*.md), so it always passed on an empty glob without
+  # opening a single Codex file. This mirrors the same four buckets
+  # (sanctioned override, matches default, drifted, unclassified) against
+  # ~/.codex/agents/plastic-*.toml instead, reading `model` and
+  # `model_reasoning_effort` as two SEPARATE lines via
+  # codex_agent_toml_model_fields, the same plain string matching
   # codex_agent_toml_well_formed? already uses (no TOML parser dependency).
-  # The expected value resolves through AgentModels::TIER_DEFAULTS mapped
-  # through AgentModels.effort_for, honoring the Codex-scoped
+  #
+  # Per the intent-186 emission contract (installer_core.rb's
+  # codex_model_fields): a tier alias writes BOTH lines, a literal Codex
+  # model id override writes `model` only. Bucket 2 (no override, basename
+  # is a TIER_DEFAULTS key) therefore compares BOTH fields, each against its
+  # own config-resolved default: the model value against
+  # AgentModels.codex_model_for(tier), the effort value against
+  # AgentModels.effort_for(tier), honoring the Codex-scoped
   # agents.models.codex.<name> override precedence install_codex's own
-  # agent_model_overrides(harness: "codex") already applies.
+  # agent_model_overrides(harness: "codex") already applies. Either field
+  # disagreeing is drift; the detail line names exactly which field(s)
+  # drifted so a model mismatch never reads as an effort mismatch or vice
+  # versa. An alias with no mapped Codex model id (codex_model_for returns
+  # nil) skips the model comparison rather than reporting drift, mirroring
+  # the installer, which still emits the effort line alone in that case.
+  #
+  # Bucket 1 (an agents.models.codex.<name> override is configured) stays
+  # sanctioned and is NEVER compared: per-agent model and effort are user
+  # configuration, per harness and per project, and can be edited after
+  # install without a reinstall, so an override must always read as
+  # healthy. This also keeps the Codex leg identical in shape to the Claude
+  # leg's four-bucket contract from intent 191.
+  #
   # AgentModels::CONSULTATION_AGENTS need no special-case bucket here:
   # generate_codex_agents already skips writing them for Codex entirely, so
   # the glob below never finds them and there is nothing to classify.
@@ -2158,21 +1377,30 @@ end
 
     installed.each do |path|
       basename = File.basename(path, ".toml")
-      installed_value = codex_agent_toml_model_value(File.read(path))
+      fields = codex_agent_toml_model_fields(File.read(path))
       override = overrides[basename]
 
       if override
-        sanctioned << "#{basename}: toml=#{installed_value.inspect}, sanctioned override=#{override.inspect}"
+        sanctioned << "#{basename}: toml model=#{fields[:model].inspect}, " \
+                      "toml effort=#{fields[:effort].inspect}, sanctioned override=#{override.inspect}"
       elsif AgentModels::TIER_DEFAULTS.key?(basename)
-        expected_effort = AgentModels.effort_for(AgentModels::TIER_DEFAULTS[basename])
-        if installed_value != expected_effort
-          drifted << "#{basename}: toml=#{installed_value.inspect}, resolved default effort=#{expected_effort.inspect}"
+        tier = AgentModels::TIER_DEFAULTS[basename]
+        expected_model = AgentModels.codex_model_for(tier)
+        expected_effort = AgentModels.effort_for(tier)
+        mismatches = []
+        if expected_model && fields[:model] != expected_model
+          mismatches << "model=#{fields[:model].inspect}, resolved default model=#{expected_model.inspect}"
         end
+        if expected_effort && fields[:effort] != expected_effort
+          mismatches << "effort=#{fields[:effort].inspect}, resolved default effort=#{expected_effort.inspect}"
+        end
+        drifted << "#{basename}: #{mismatches.join("; ")}" if mismatches.any?
       else
-        unclassified << "#{basename}: toml=#{installed_value.inspect}, no resolved default (basename is in " \
-                         "neither AgentModels::TIER_DEFAULTS nor AgentModels::CONSULTATION_AGENTS in " \
-                         "scripts/lib/agent_models.rb; add it there, or set agents.models.codex.#{basename} " \
-                         "to sanction a model explicitly)"
+        unclassified << "#{basename}: toml model=#{fields[:model].inspect}, " \
+                        "toml effort=#{fields[:effort].inspect}, no resolved default (basename is in " \
+                        "neither AgentModels::TIER_DEFAULTS nor AgentModels::CONSULTATION_AGENTS in " \
+                        "scripts/lib/agent_models.rb; add it there, or set agents.models.codex.#{basename} " \
+                        "to sanction a model explicitly)"
       end
     end
 
@@ -2189,7 +1417,7 @@ end
       )]
     else
       parts = []
-      parts << "#{drifted.size} installed Codex agent TOML(s) have unsanctioned model drift vs the config-resolved default" if drifted.any?
+      parts << "#{drifted.size} installed Codex agent TOML(s) have unsanctioned model or effort drift vs the config-resolved default" if drifted.any?
       parts << "#{unclassified.size} installed Codex agent TOML(s) have no resolved default in scripts/lib/agent_models.rb" if unclassified.any?
       [check(
         category: "core_files", name: "agent_model_drift", status: "warn",
@@ -2209,69 +1437,6 @@ end
   # Manifest format: { "version", "created", "files": { abs_path => sha256 } }.
   # A missing manifest is a fail; any missing/mismatched listed file is a fail;
   # otherwise a single pass per manifest.
-  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
 
   # install_integrity (intent 210, D4): FULL tier only, warn-only, never writes. For each
   # installed agent, re-hash its manifest-listed files against disk and WARN on drift
@@ -2340,50 +1505,6 @@ end
   # mirror (~/.plastic/projects/<slug>/{store,INDEX.md,project.yml}); this method validates the
   # registered repo path itself (projects.yml's "path" key), decoupled from 175's deeper
   # repo-root-versus-registered-path question (219 D9).
-  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
 
   # Per-project validation extracted from check_project_stores so a single
   # project can be checked in isolation (used by `--store <slug>`).
@@ -2776,6 +1897,61 @@ end
     end
   end
 
+  # --- Check category: runtime (which ruby a spawned hook resolves) ---
+  #
+  # Intent 235, D6. REPORT ONLY: this check never pins an interpreter and never repairs.
+  # A hook is launched by the agent application, not by a login shell, so a version
+  # manager that activates on shell prompt render (mise, rbenv, asdf) may never reach it
+  # and bare `ruby` can still resolve to the system interpreter long after the user
+  # installs a modern Ruby.
+  #
+  # Below the floor is a WARN, never a fail. Doctor cannot know that the PATH it sees is
+  # the PATH the agent application will hand its hooks, so it reports the risk with a
+  # precise fix hint instead of blocking. "Could not determine" is the same warn: an
+  # honest unknown, not a silent pass.
+  #
+  # The probe is injected as a keyword with a real default (see check_serena for the same
+  # shape), so tests never spawn a process and never touch ENV.
+  def check_ruby_runtime(probe: RubyProbe.method(:resolve))
+    resolved = probe.call
+    version = resolved[:version]
+    parsed = version && safe_version(version)
+
+    if parsed.nil?
+      return [check(
+        category: "runtime", name: "ruby_floor", status: "warn",
+        message: "Could not determine which ruby a Plastic hook would resolve on PATH " \
+                 "(no runnable `ruby` answered), so Plastic cannot confirm hook processes " \
+                 "meet the Ruby #{Preflight::RUBY_FLOOR} floor",
+        fixable: false,
+        fix_hint: "Make sure `ruby -v` works, then pin one for the whole machine: " \
+                  "mise use --global ruby@#{Preflight::RUBY_PIN}"
+      )]
+    end
+
+    where = resolved[:path].to_s.empty? ? "ruby on PATH" : resolved[:path]
+
+    if parsed < safe_version(Preflight::RUBY_FLOOR)
+      return [check(
+        category: "runtime", name: "ruby_floor", status: "warn",
+        message: "Hooks would resolve Ruby #{version} at #{where}, below Plastic's floor of " \
+                 "#{Preflight::RUBY_FLOOR}. Hook scripts can fail on this interpreter even when " \
+                 "your own shell has a newer Ruby, because a shell-activated version manager " \
+                 "does not reach a hook process spawned by the agent application",
+        details: [where],
+        fixable: false,
+        fix_hint: "Pin a Ruby the whole machine sees: mise use --global ruby@#{Preflight::RUBY_PIN}"
+      )]
+    end
+
+    [check(
+      category: "runtime", name: "ruby_floor", status: "pass",
+      message: "Hooks would resolve Ruby #{version} at #{where}, at or above Plastic's floor " \
+               "of #{Preflight::RUBY_FLOOR}",
+      details: [where]
+    )]
+  end
+
   # --- Check category: skill-lint (advisory only; intent 85b) ---
   #
   # Reports SkillLint's five structural checks over the skills/ tree as a
@@ -2829,6 +2005,7 @@ end
     all_checks += check_deprecations
     all_checks += check_config_asks(agent_key)
     all_checks += check_qmd
+    all_checks += check_ruby_runtime
     all_checks += check_done_signals(scopes: ["global"])
     all_checks += check_skill_lint
     all_checks += check_install_integrity
@@ -2836,22 +2013,6 @@ end
     summarize(all_checks, agent_key)
   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
-
   # Per-intent structure gate for `doctor.rb --intent <id> [--store <key>] [--disposition ...]`
   # (intent 222). `store`, here, is already the resolved scope key (see
   # normalize_intent_store_scope, the CLI-boundary translator that turns the loosely-typed
@@ -2945,33 +2106,6 @@ end
       check_enola(cwd: probe_cwd, path_probe: enola_path_probe, marker_finder: enola_marker_finder)
   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
 
   # --- Main ---