diff --git a/scripts/doctor.ps1 b/scripts/doctor.ps1
index 043263e..37f3c22 100644
--- a/scripts/doctor.ps1
+++ b/scripts/doctor.ps1
@@ -2,16 +2,67 @@
 param()
 $ErrorActionPreference = 'Stop'
 $root = Split-Path $PSScriptRoot -Parent
+. (Join-Path $PSScriptRoot 'lib/manifest.ps1')
 $homePath = [Environment]::GetFolderPath('UserProfile')
 $fail = $false
 function Result($state, $message) { Write-Output ("$state $message"); if ($state -eq 'FAIL') { $script:fail = $true } }
+
 foreach ($tool in @('codex','claude')) { if (Get-Command $tool -ErrorAction SilentlyContinue) { $version = & $tool --version 2>&1 | Select-Object -First 1; Result 'PASS' "$tool available ($version)" } else { Result 'WARN' "$tool unavailable" } }
 if ($PSVersionTable.PSVersion.Major -ge 6 -and -not $IsWindows) { if (Get-Command jq -ErrorAction SilentlyContinue) { Result 'PASS' 'jq available for Claude status line' } else { Result 'WARN' 'jq unavailable; Claude status line is disabled' } }
+
+$sourceAgentCount = @(Get-ChildItem (Join-Path $root 'shared/agents') -Directory -ErrorAction SilentlyContinue).Count
+$sourceSkillCount = @(Get-ChildItem (Join-Path $root 'shared/skills') -Filter 'SKILL.md' -Recurse -ErrorAction SilentlyContinue).Count
+$ruleSkillManifestPath = Join-Path $root 'adapters/claude/rule-skills.tsv'
+$ruleSkillCount = if (Test-Path -LiteralPath $ruleSkillManifestPath) { @(Import-Csv -LiteralPath $ruleSkillManifestPath -Delimiter ([char]9)).Count } else { 0 }
+
 foreach ($platform in @('windows','linux')) {
-if (Test-Path (Join-Path $root "generated/codex-$platform/AGENTS.md")) { Result 'PASS' 'generated output present' } else { Result 'FAIL' 'generated output missing; run build' }
-if ((Test-Path (Join-Path $root "generated/codex-$platform/hooks/scripts/Validate-CommandSafety.ps1")) -and (Test-Path (Join-Path $root "generated/codex-$platform/hooks/scripts/validate-command-safety.sh")) -and (Test-Path (Join-Path $root "generated/claude-$platform/hooks/scripts/Validate-CommandSafety.ps1")) -and (Test-Path (Join-Path $root "generated/claude-$platform/hooks/scripts/validate-command-safety.sh"))) { Result 'PASS' 'generated hooks present' } else { Result 'FAIL' 'generated hooks missing; run build' }
+    if (Test-Path (Join-Path $root "generated/codex-$platform/AGENTS.md")) { Result 'PASS' "generated output present ($platform)" } else { Result 'FAIL' "generated output missing ($platform); run build" }
+    if ((Test-Path (Join-Path $root "generated/codex-$platform/hooks/scripts/Validate-CommandSafety.ps1")) -and (Test-Path (Join-Path $root "generated/codex-$platform/hooks/scripts/validate-command-safety.sh")) -and (Test-Path (Join-Path $root "generated/claude-$platform/hooks/scripts/Validate-CommandSafety.ps1")) -and (Test-Path (Join-Path $root "generated/claude-$platform/hooks/scripts/validate-command-safety.sh"))) { Result 'PASS' "generated hooks present ($platform)" } else { Result 'FAIL' "generated hooks missing ($platform); run build" }
+    foreach ($client in @('codex','claude')) {
+        $package = Join-Path $root "generated/$client-$platform"
+        if (-not (Test-Path $package)) { continue }
+        $agentCount = @(Get-ChildItem (Join-Path $package 'agents') -File -ErrorAction SilentlyContinue).Count
+        if ($agentCount -eq $sourceAgentCount) { Result 'PASS' "$client-$platform agent count matches source ($agentCount)" } else { Result 'FAIL' "$client-$platform agent count $agentCount does not match source ($sourceAgentCount)" }
+        $expectedSkillCount = if ($client -eq 'claude') { $sourceSkillCount + $ruleSkillCount } else { $sourceSkillCount }
+        $skillCount = @(Get-ChildItem (Join-Path $package 'skills') -Filter 'SKILL.md' -Recurse -ErrorAction SilentlyContinue).Count
+        if ($skillCount -eq $expectedSkillCount) { Result 'PASS' "$client-$platform skill count matches source ($skillCount)" } else { Result 'FAIL' "$client-$platform skill count $skillCount does not match source ($expectedSkillCount)" }
+        $placeholderHits = @(Get-ChildItem $package -File -Recurse | Where-Object { ((Get-Content -LiteralPath $_.FullName -Raw) -replace '__AI_CONFIG_ROOT__', '') -cmatch '__[A-Z0-9_]+__' })
+        if ($placeholderHits.Count -eq 0) { Result 'PASS' "$client-$platform has no unresolved placeholders" } else { Result 'FAIL' "$client-$platform has unresolved placeholders: $($placeholderHits.FullName -join ', ')" }
+    }
 }
-foreach ($path in @('.codex/AGENTS.md','.codex/config.toml','.claude/CLAUDE.md','.claude/settings.json')) { if (Test-Path (Join-Path $homePath $path)) { Result 'PASS' "installed $path" } else { Result 'WARN' "not installed $path" } }
+
+foreach ($path in @('.codex/AGENTS.md','.codex/config.toml','.claude/CLAUDE.md','.claude/settings.json')) {
+    if (Test-Path (Join-Path $homePath $path)) { Result 'PASS' "installed $path" } else { Result 'WARN' "not installed $path" }
+}
+
+$settingsPath = Join-Path $homePath '.claude/settings.json'
+if (Test-Path -LiteralPath $settingsPath) {
+    try { Get-Content -LiteralPath $settingsPath -Raw | ConvertFrom-Json | Out-Null; Result 'PASS' 'installed .claude/settings.json is valid JSON' }
+    catch { Result 'FAIL' 'installed .claude/settings.json is not valid JSON' }
+}
+$configTomlPath = Join-Path $homePath '.codex/config.toml'
+if (Test-Path -LiteralPath $configTomlPath) {
+    $tomlContent = Get-Content -LiteralPath $configTomlPath -Raw
+    $balanced = (([regex]::Matches($tomlContent, '(?<!\\)"')).Count % 2 -eq 0) -and (([regex]::Matches($tomlContent, '\[')).Count -eq ([regex]::Matches($tomlContent, '\]')).Count)
+    if ($balanced) { Result 'PASS' 'installed .codex/config.toml looks structurally valid' } else { Result 'FAIL' 'installed .codex/config.toml has unbalanced quotes or brackets' }
+}
+
+foreach ($destination in @((Join-Path $homePath '.codex'), (Join-Path $homePath '.agents/skills'), (Join-Path $homePath '.claude'))) {
+    $manifestPath = Get-ManagedManifestPath $destination
+    if (-not (Test-Path -LiteralPath $manifestPath)) { continue }
+    $manifest = Read-ManagedManifest $manifestPath
+    $missing = @()
+    $modified = @()
+    foreach ($relative in $manifest.Keys) {
+        $target = Join-Path $destination $relative
+        if (-not (Test-Path -LiteralPath $target)) { $missing += $relative; continue }
+        if ((Get-Sha256Hash $target) -ne $manifest[$relative]) { $modified += $relative }
+    }
+    if ($missing.Count) { Result 'WARN' "$destination is missing managed files: $($missing -join ', ')" } else { Result 'PASS' "$destination has no missing managed files" }
+    if ($modified.Count) { Result 'WARN' "$destination has locally modified managed files: $($modified -join ', ')" } else { Result 'PASS' "$destination has no locally modified managed files" }
+}
+
 foreach ($path in @('shared/rules','shared/skills','shared/agents','shared/hooks/scripts')) { if (Test-Path (Join-Path $root $path)) { Result 'PASS' "source $path" } else { Result 'FAIL' "missing $path" } }
+
 if ($fail) { exit 1 }
 Write-Output 'PASS doctor'