feat!: unify sandbox configuration and permission application

Replace the split executable approval and sandbox resolution workflows with schema_version 2 and a YAML-driven execution.entries model. Resolve workspace, mount, executable, runtime, network, and resource settings into one config-scoped Applied Configuration snapshot protected by a user-only DACL and written with atomic replacement.

Reduce the public CLI to implicit server startup, show, and apply. Remove serve/check, executable and sandbox subcommands, and configuration override flags including --config, --lang, --transport, --path, and --runtime-root. Add migration diagnostics for every removed schema and command surface, and keep server preflight mandatory for both stdio and HTTP.

Update effective-policy compilation to validate the applied fingerprint, resolved paths, and executable hashes before startup. Preserve fail-closed behavior while allowing execution entries and runtime roots inside a development workspace to inherit that workspace capability without creating an impossible narrower ACL boundary.

Rewrite the README around the consolidated permission matrix and document configuration, application, store location, startup, transport-specific elevation, Python 3.14, PowerShell, and cmd usage. Align specifications, design, implementation plan, traceability, audit report, localization, publish scripts, and operational verification with the breaking schema.

Verification: Release build completed with zero warnings and errors; Agent.Core.Tests 104/104 and Agent.Planner.Tests 10/10 passed; administrator Windows Security/Recovery 56/56 and README operational 19/19 passed with no skips; published HTTP MCP completed a cmd/curl/venv-Python task with network deny and zero ACL, WFP, journal, backup, or process residue.

7 files changed, 98 insertions, 224 deletions

diff --git a/scripts/E2EClient/Program.cs b/scripts/E2EClient/Program.cs
index ee7bb75..8733cdf 100644
--- a/scripts/E2EClient/Program.cs
+++ b/scripts/E2EClient/Program.cs
@@ -13,7 +13,7 @@ IClientTransport transport = args[0] == "stdio"
     {
         Name = "agent-mcp-operational-e2e",
         Command = Path.GetFullPath(args[1]),
-        Arguments = ["serve", "--config", Path.GetFullPath(args[2]), "--lang", "ja", "--transport", "stdio"],
+        Arguments = [Path.GetFullPath(args[2])],
         WorkingDirectory = Path.GetDirectoryName(Path.GetFullPath(args[1]))!
     })
     : new HttpClientTransport(new HttpClientTransportOptions
diff --git a/scripts/Operational-E2E.ps1 b/scripts/Operational-E2E.ps1
index b253198..cea1c75 100644
--- a/scripts/Operational-E2E.ps1
+++ b/scripts/Operational-E2E.ps1
@@ -17,8 +17,7 @@ $bundleRoot = Join-Path $root 'bundle'
 $fixture = Join-Path $root 'fixture'
 $alias = 'python-e2e-' + [Guid]::NewGuid().ToString('N').Substring(0, 12)
 $passed = $false
-$approved = $false
-$resolutionStorePath = $null
+$appliedStorePath = $null
 $server = $null
 New-Item -ItemType Directory -Path $bundleRoot,$fixture | Out-Null
 $fixtureAclBefore = (Get-Acl -LiteralPath $fixture).Sddl
@@ -40,6 +39,8 @@ try {
     $pythonVersion = (& $python --version 2>&1 | Out-String).Trim()
     if ($pythonVersion -notmatch '^Python 3\.14\.') { throw "Operational E2E requires Python 3.14; resolved '$pythonVersion'." }
     $runtimeRoot = Split-Path $python
+    $pythonYaml = $pythonLogical.Replace('\','/')
+    $runtimeYaml = $runtimeRoot.Replace('\','/')
 
     Set-Content -LiteralPath (Join-Path $fixture 'README.md') -Encoding utf8NoBOM -Value @'
 # Graph metrics fixture
@@ -50,7 +51,7 @@ produce a deterministic topological order, detect cycles, and calculate the weig
 
     $fixtureYaml = $fixture.Replace('\','/')
     $config = @"
-schema_version: 1
+schema_version: 2
 application:
   language: ja
 mcp:
@@ -83,9 +84,10 @@ sandbox:
     - $fixtureYaml
   mounts: []
   execution:
-    executables:
-      - $alias
-    shells: []
+    entries:
+      - alias: $alias
+        path: $pythonYaml
+        runtime_root: $runtimeYaml
   network:
     access: none
     local_endpoints: []
@@ -112,15 +114,12 @@ logging:
 "@
     Set-Content -LiteralPath $configPath -Value $config -Encoding utf8NoBOM
 
-    & $agent executable approve $alias --path $pythonLogical --runtime-root $runtimeRoot --yes --config $configPath --lang en
-    if ($LASTEXITCODE -ne 0) { throw 'Executable approval failed.' }
-    $approved = $true
-    & $agent sandbox confirm --yes --config $configPath --lang en
-    if ($LASTEXITCODE -ne 0) { throw 'Sandbox Environment Resolution confirmation failed.' }
+    & $agent apply $configPath --yes
+    if ($LASTEXITCODE -ne 0) { throw 'Applied Configuration failed.' }
     $normalizedConfig = [IO.Path]::GetFullPath($configPath).ToUpperInvariant()
     $hash = [Convert]::ToHexString([Security.Cryptography.SHA256]::HashData([Text.Encoding]::UTF8.GetBytes($normalizedConfig)))
-    $resolutionStorePath = Join-Path $env:LOCALAPPDATA "AgentSandboxMcp\environment-resolutions\$hash.json"
-    & $agent sandbox show --format json --config $configPath --lang en | Out-Null
+    $appliedStorePath = Join-Path $env:LOCALAPPDATA "AgentSandboxMcp\applied-configurations\$hash.json"
+    & $agent show $configPath | Out-Null
     if ($LASTEXITCODE -ne 0) { throw 'Effective Sandbox Policy show failed.' }
 
     $request = @"
@@ -138,7 +137,7 @@ README.md の読取後、2ファイルの作成、最初のテスト実行、失
         if ($LASTEXITCODE -ne 0) { throw 'E2E stdio client failed.' }
     }
     else {
-        $server = Start-Process -FilePath $agent -ArgumentList @('serve','--config',$configPath,'--lang','ja','--transport','http') -WorkingDirectory $bundle -WindowStyle Hidden -PassThru
+        $server = Start-Process -FilePath $agent -ArgumentList @($configPath) -WorkingDirectory $bundle -WindowStyle Hidden -PassThru
         $httpAuthority = if ($HttpHost -eq '::1') { '[::1]' } else { $HttpHost }
         $endpoint = "http://${httpAuthority}:18080/mcp"
         $ready = $false
@@ -183,11 +182,8 @@ catch {
 }
 finally {
     if ($server -and -not $server.HasExited) { $server.Kill($true); $server.WaitForExit() }
-    if ($approved -and (Test-Path -LiteralPath $agent)) {
-        & $agent executable revoke $alias --yes --config $configPath --lang en | Out-Null
-    }
-    if ($resolutionStorePath -and (Test-Path -LiteralPath $resolutionStorePath)) {
-        Remove-Item -LiteralPath $resolutionStorePath -Force
+    if ($appliedStorePath -and (Test-Path -LiteralPath $appliedStorePath)) {
+        Remove-Item -LiteralPath $appliedStorePath -Force
     }
     if ($passed -and (Test-Path -LiteralPath $root)) { Remove-Item -LiteralPath $root -Recurse -Force }
 }
diff --git a/scripts/Publish-Release.ps1 b/scripts/Publish-Release.ps1
index d794bb5..41bdfa3 100644
--- a/scripts/Publish-Release.ps1
+++ b/scripts/Publish-Release.ps1
@@ -66,8 +66,8 @@ try {
     if (-not $SkipRuntimeCheck) {
         Push-Location $freshBundle
         try {
-            & .\agent-mcp.exe sandbox resolve --config .\agent.yaml --lang en
-            if ($LASTEXITCODE -ne 0) { throw "Bundle resolution check failed with exit code $LASTEXITCODE." }
+            & .\agent-mcp.exe show .\agent.yaml
+            if ($LASTEXITCODE -ne 0) { throw "Bundle configuration check failed with exit code $LASTEXITCODE." }
         }
         finally { Pop-Location }
     }
diff --git a/scripts/Restart-PublishedServer.ps1 b/scripts/Restart-PublishedServer.ps1
index 58dd928..d4386f4 100644
--- a/scripts/Restart-PublishedServer.ps1
+++ b/scripts/Restart-PublishedServer.ps1
@@ -26,5 +26,5 @@ if ($StopOnly) { exit 0 }
 if (-not (Test-Path -LiteralPath $agent) -or -not (Test-Path -LiteralPath $configuration)) {
     throw 'Published agent-mcp executable or configuration is missing.'
 }
-$started = Start-Process -FilePath $agent -ArgumentList @('serve', '--config', $configuration) -WorkingDirectory $bundle -WindowStyle Hidden -PassThru
+$started = Start-Process -FilePath $agent -ArgumentList @($configuration) -WorkingDirectory $bundle -WindowStyle Hidden -PassThru
 Write-Output "Started published agent-mcp PID $($started.Id)."
diff --git a/scripts/Run-Final-ElevatedVerification.ps1 b/scripts/Run-Final-ElevatedVerification.ps1
index 627bd65..71135c2 100644
--- a/scripts/Run-Final-ElevatedVerification.ps1
+++ b/scripts/Run-Final-ElevatedVerification.ps1
@@ -47,8 +47,8 @@ $windowsTests = Join-Path $repository 'build\Release\Agent.Windows.Tests\net10.0
 $coreTests = Join-Path $repository 'build\Release\Agent.Core.Tests\net10.0-windows10.0.26100.0\Agent.Core.Tests.exe'
 $plannerTests = Join-Path $repository 'build\Release\Agent.Planner.Tests\net10.0\Agent.Planner.Tests.exe'
 
-Invoke-VerificationStep 'bundle-check' {
-    & (Join-Path $bundle 'agent-mcp.exe') check --config (Join-Path $bundle 'agent.yaml') --lang en
+Invoke-VerificationStep 'bundle-show' {
+    & (Join-Path $bundle 'agent-mcp.exe') show (Join-Path $bundle 'agent.yaml')
 }
 Invoke-VerificationStep 'windows-security-tests' { & $windowsTests }
 Invoke-VerificationStep 'core-unit-integration-tests' { & $coreTests }
diff --git a/scripts/Verify-PublishedHttp.ps1 b/scripts/Verify-PublishedHttp.ps1
index a02a28b..7dd5fe2 100644
--- a/scripts/Verify-PublishedHttp.ps1
+++ b/scripts/Verify-PublishedHttp.ps1
@@ -29,6 +29,8 @@ $runRoot = Join-Path $testRootPath ('agent-mcp-http-cmd-' + [Guid]::NewGuid().To
 $runRootForward = $runRoot.Replace('\', '/')
 $endpoint = 'http://127.0.0.1:8080/mcp'
 $log = Join-Path $evidence 'verification.log'
+$serverOut = Join-Path $evidence 'server.stdout.log'
+$serverErr = Join-Path $evidence 'server.stderr.log'
 $server = $null
 New-Item -ItemType Directory -Force -Path $evidence | Out-Null
 New-Item -ItemType Directory -Path $runRoot | Out-Null
@@ -47,14 +49,17 @@ run-probe.cmdは次を順番に実行し、どれかが失敗したら非0で終
 "@
 
 try {
-    & $agent check --config $config --lang ja 2>&1 | Tee-Object -FilePath $log
-    if ($LASTEXITCODE -ne 0) { throw "Published check failed with exit code $LASTEXITCODE." }
+    & $agent show $config 2>&1 | Tee-Object -FilePath $log
+    if ($LASTEXITCODE -ne 0) { throw "Published configuration show failed with exit code $LASTEXITCODE." }
 
-    $server = Start-Process -FilePath $agent -ArgumentList @('serve','--config',$config,'--lang','ja','--transport','http') `
-        -WorkingDirectory $bundle -WindowStyle Hidden -PassThru
+    $server = Start-Process -FilePath $agent -ArgumentList @($config) -WorkingDirectory $bundle `
+        -WindowStyle Hidden -RedirectStandardOutput $serverOut -RedirectStandardError $serverErr -PassThru
     $ready = $false
     for ($attempt = 0; $attempt -lt 100; $attempt++) {
-        if ($server.HasExited) { throw "Published server exited before readiness: $($server.ExitCode)" }
+        if ($server.HasExited) {
+            $diagnostic = if (Test-Path -LiteralPath $serverErr) { Get-Content -LiteralPath $serverErr -Raw } else { '' }
+            throw "Published server exited before readiness: $($server.ExitCode) $diagnostic"
+        }
         try {
             $response = Invoke-WebRequest -Uri $endpoint -Method Get -SkipHttpErrorCheck
             if ($response.StatusCode -eq 405) { $ready = $true; break }
diff --git a/scripts/Verify-Readme.ps1 b/scripts/Verify-Readme.ps1
index f67f640..42c8b8f 100644
--- a/scripts/Verify-Readme.ps1
+++ b/scripts/Verify-Readme.ps1
@@ -1,255 +1,128 @@
 param(
-    [Parameter(Mandatory)]
-    [string]$TestRoot,
-    [Parameter(Mandatory)]
-    [string]$VenvPython,
+    [Parameter(Mandatory)][string]$TestRoot,
+    [Parameter(Mandatory)][string]$VenvPython,
     [string]$EvidenceRoot = 'artifacts\evidence\readme-verification',
     [switch]$CliOnly
 )
 
 $ErrorActionPreference = 'Stop'
-$OutputEncoding = [Text.UTF8Encoding]::new($false)
-[Console]::OutputEncoding = $OutputEncoding
 $repository = (Resolve-Path (Join-Path $PSScriptRoot '..')).Path
 $testRootPath = (Resolve-Path -LiteralPath $TestRoot).Path
 $venvPythonPath = (Resolve-Path -LiteralPath $VenvPython).Path
 $evidence = [IO.Path]::GetFullPath((Join-Path $repository $EvidenceRoot))
-if (-not $evidence.StartsWith($repository + [IO.Path]::DirectorySeparatorChar, [StringComparison]::OrdinalIgnoreCase)) {
-    throw 'Evidence output must remain inside the repository.'
-}
-$administrator = ([Security.Principal.WindowsPrincipal][Security.Principal.WindowsIdentity]::GetCurrent()).IsInRole(
-    [Security.Principal.WindowsBuiltInRole]::Administrator)
-if (-not $administrator -and -not $CliOnly) { throw 'README verification must run as Windows Administrator unless -CliOnly is specified.' }
-if (-not (Test-Path -LiteralPath $venvPythonPath -PathType Leaf)) { throw 'VenvPython must be an existing file.' }
+if (-not $evidence.StartsWith($repository + [IO.Path]::DirectorySeparatorChar, [StringComparison]::OrdinalIgnoreCase)) { throw 'Evidence output must remain inside the repository.' }
+$administrator = ([Security.Principal.WindowsPrincipal][Security.Principal.WindowsIdentity]::GetCurrent()).IsInRole([Security.Principal.WindowsBuiltInRole]::Administrator)
+if (-not $administrator -and -not $CliOnly) { throw 'README operational verification must run as Windows Administrator.' }
 
 $pwshPath = (Get-Command pwsh.exe -ErrorAction Stop).Source
-$pwshRuntime = Split-Path $pwshPath
 $cmdPath = $env:ComSpec
 $venvRoot = Split-Path (Split-Path $venvPythonPath)
-$pyvenv = Get-Content -LiteralPath (Join-Path $venvRoot 'pyvenv.cfg')
-$pythonRuntime = (($pyvenv | Where-Object { $_ -match '^home\s*=' }) -split '=', 2)[1].Trim()
-if (-not (Test-Path -LiteralPath $pythonRuntime -PathType Container)) { throw "Python Runtime Root does not exist: $pythonRuntime" }
+$pythonRuntime = (((Get-Content -LiteralPath (Join-Path $venvRoot 'pyvenv.cfg')) | Where-Object { $_ -match '^home\s*=' }) -split '=', 2)[1].Trim()
 $basePythonPath = Join-Path $pythonRuntime 'python.exe'
 if (-not (Test-Path -LiteralPath $basePythonPath -PathType Leaf)) { throw "Base Python does not exist: $basePythonPath" }
 
 New-Item -ItemType Directory -Force -Path $evidence | Out-Null
-$runRoot = Join-Path $testRootPath ('agent-mcp-readme-cli-' + [Guid]::NewGuid().ToString('N'))
+$runRoot = Join-Path $testRootPath ('agent-mcp-readme-' + [Guid]::NewGuid().ToString('N'))
 New-Item -ItemType Directory -Path $runRoot | Out-Null
 $agent = Join-Path $repository 'build\Release\Agent.App\net10.0-windows10.0.26100.0\agent-mcp.exe'
 $windowsTests = Join-Path $repository 'build\Release\Agent.Windows.Tests\net10.0-windows10.0.26100.0\Agent.Windows.Tests.exe'
 $configPath = Join-Path $runRoot 'agent.yaml'
 $logPath = Join-Path $evidence 'verification.log'
-$failed = $false
-$aliases = @(
-    ('readme-python-' + [Guid]::NewGuid().ToString('N').Substring(0, 8))
-    ('readme-powershell-' + [Guid]::NewGuid().ToString('N').Substring(0, 8))
-    ('readme-cmd-' + [Guid]::NewGuid().ToString('N').Substring(0, 8))
-)
-$pythonAlias, $powershellAlias, $cmdAlias = $aliases
-$listener = [Net.Sockets.TcpListener]::new([Net.IPAddress]::Loopback, 0)
-$listener.Start()
-$httpPort = ([Net.IPEndPoint]$listener.LocalEndpoint).Port
-$listener.Stop()
-$resolutionStorePath = $null
 $server = $null
+$failed = $false
 
-function Invoke-Step {
-    param([string]$Name, [scriptblock]$Action)
+function Invoke-Step([string]$Name, [scriptblock]$Action) {
     "START $Name $(Get-Date -Format o)" | Tee-Object -FilePath $logPath -Append
     try {
         $global:LASTEXITCODE = 0
         & $Action *>&1 | Tee-Object -FilePath $logPath -Append
         if ($LASTEXITCODE -ne 0) { throw "$Name exited with $LASTEXITCODE" }
-        "PASS $Name $(Get-Date -Format o)" | Tee-Object -FilePath $logPath -Append
-    }
-    catch {
-        $_ | Out-String | Tee-Object -FilePath $logPath -Append
-        $script:failed = $true
-        "FAIL $Name $(Get-Date -Format o)" | Tee-Object -FilePath $logPath -Append
-    }
+        "PASS $Name" | Tee-Object -FilePath $logPath -Append
+    } catch { $script:failed = $true; "FAIL $Name $($_.Exception.Message)" | Tee-Object -FilePath $logPath -Append }
 }
 
-function Invoke-ExpectedFailure {
-    param([string]$Name, [string[]]$Arguments)
-    "START $Name $(Get-Date -Format o)" | Tee-Object -FilePath $logPath -Append
+function Invoke-ExpectedFailure([string]$Name, [string[]]$Arguments) {
     & $agent @Arguments *>&1 | Tee-Object -FilePath $logPath -Append
-    if ($LASTEXITCODE -ne 2) {
-        $script:failed = $true
-        "FAIL $Name expected_exit=2 actual_exit=$LASTEXITCODE" | Tee-Object -FilePath $logPath -Append
-    }
-    else { "PASS $Name expected_exit=2" | Tee-Object -FilePath $logPath -Append }
-}
-
-function Start-And-ProbeServer {
-    param([bool]$ExplicitServe)
-    $arguments = if ($ExplicitServe) {
-        @('serve', '--config', $configPath, '--lang', 'ja', '--transport', 'http')
-    } else {
-        @('--config', $configPath, '--lang', 'ja', '--transport', 'http')
-    }
-    $script:server = Start-Process -FilePath $agent -ArgumentList $arguments -WorkingDirectory (Split-Path $agent) -WindowStyle Hidden -PassThru
-    $endpoint = "http://127.0.0.1:$httpPort/mcp"
-    for ($attempt = 0; $attempt -lt 100; $attempt++) {
-        if ($script:server.HasExited) { throw "Server exited before becoming ready: $($script:server.ExitCode)" }
-        try {
-            $response = Invoke-WebRequest -Uri $endpoint -Method Get -SkipHttpErrorCheck
-            if ($response.StatusCode -eq 405) { return }
-        } catch { }
-        Start-Sleep -Milliseconds 100
-    }
-    throw 'Server did not become ready.'
+    if ($LASTEXITCODE -ne 2) { $script:failed = $true; "FAIL $Name expected=2 actual=$LASTEXITCODE" | Tee-Object -FilePath $logPath -Append }
+    else { "PASS $Name" | Tee-Object -FilePath $logPath -Append }
 }
 
 try {
-    $forwardRoot = $testRootPath.Replace('\', '/')
-    $forwardPrompt = (Join-Path $repository 'prompts\user-system.md').Replace('\', '/')
-    $forwardSkills = (Join-Path $repository 'skills').Replace('\', '/')
-    $forwardLocales = (Join-Path $repository 'config\locales').Replace('\', '/')
-    $forwardLogs = (Join-Path $runRoot 'logs').Replace('\', '/')
+    $listener = [Net.Sockets.TcpListener]::new([Net.IPAddress]::Loopback, 0); $listener.Start()
+    $httpPort = ([Net.IPEndPoint]$listener.LocalEndpoint).Port; $listener.Stop()
+    $forwardRoot = $testRootPath.Replace('\','/')
+    $forwardPrompt = (Join-Path $repository 'prompts\user-system.md').Replace('\','/')
+    $forwardSkills = (Join-Path $repository 'skills').Replace('\','/')
+    $forwardLocales = (Join-Path $repository 'config\locales').Replace('\','/')
+    $forwardLogs = (Join-Path $runRoot 'logs').Replace('\','/')
+    $pythonYaml = $basePythonPath.Replace('\','/'); $runtimeYaml = $pythonRuntime.Replace('\','/')
+    $pwshYaml = $pwshPath.Replace('\','/'); $cmdYaml = $cmdPath.Replace('\','/')
     @"
-schema_version: 1
-application:
-  language: en
+schema_version: 2
+application: { language: en }
 mcp:
   transport: http
-  http:
-    host: 127.0.0.1
-    port: $httpPort
-  images:
-    max_count: 4
-    max_bytes_each: 10485760
-    max_total_bytes: 20971520
-  tasks:
-    time_to_live_hours: 24
-    poll_interval_ms: 1000
-agent:
-  user_system_prompt: $forwardPrompt
-  max_iterations: 8
-  same_failure_limit: 2
-ollama:
-  endpoint: http://127.0.0.1:11434
-  model: deepseek-v4-flash:cloud
-  think: true
-  keep_alive: 5m
-  options:
-    num_ctx: 32768
-    temperature: 0
-  extra_options: {}
-planner:
-  max_tasks: 8
+  http: { host: 127.0.0.1, port: $httpPort }
+agent: { user_system_prompt: $forwardPrompt, max_iterations: 8, same_failure_limit: 2 }
+ollama: { endpoint: 'http://127.0.0.1:11434', model: 'deepseek-v4-flash:cloud', think: true }
+planner: { max_tasks: 8 }
 sandbox:
   profile: development
-  workspaces:
-    - $forwardRoot
+  workspaces: [$forwardRoot]
   mounts: []
   execution:
-    executables:
-      - $pythonAlias
-    shells:
-      - $powershellAlias
-      - $cmdAlias
-  network:
-    access: none
-    local_endpoints: []
-    restricted_endpoints: []
-  resources:
-    profile: constrained
-file_edit:
-  memory_backup_limit_mb: 16
-limits:
-  whole_read_bytes: 1048576
-  search_max_results: 1000
-  tail_max_lines: 10000
-  context_summary_ratio: 0.8
-localization:
-  directory: $forwardLocales
-  fallback: en
-skills:
-  directory: $forwardSkills
-logging:
-  directory: $forwardLogs
-  level: information
-  http_requests: true
-  max_file_bytes: 10485760
-  retained_files: 5
+    entries:
+      - { alias: python, path: $pythonYaml, runtime_root: $runtimeYaml }
+      - { alias: powershell, path: '$pwshYaml' }
+      - { alias: cmd, path: $cmdYaml }
+  network: { access: none, local_endpoints: [], restricted_endpoints: [] }
+  resources: { profile: constrained }
+localization: { directory: $forwardLocales, fallback: en }
+skills: { directory: $forwardSkills }
+logging: { directory: $forwardLogs, level: information, max_file_bytes: 10485760, retained_files: 5 }
 "@ | Set-Content -LiteralPath $configPath -Encoding utf8NoBOM
 
-    @(
-        "timestamp=$(Get-Date -Format o)",
-        "commit=$(git -C $repository rev-parse HEAD)",
-        "administrator=$administrator",
-        "os=$([Environment]::OSVersion.VersionString)",
-        "venv_python=$venvPythonPath",
-        "venv_version=$(& $venvPythonPath --version)",
-        "powershell=$pwshPath",
-        "cmd=$cmdPath"
-    ) | Set-Content -LiteralPath (Join-Path $evidence 'metadata.txt') -Encoding utf8NoBOM
-
-    Invoke-Step 'cli-sandbox-resolve' { & $agent sandbox resolve --config $configPath --lang ja }
-    Invoke-Step 'cli-sandbox-confirm-yes' { & $agent sandbox confirm --yes --config $configPath --lang ja }
     $normalizedConfig = [IO.Path]::GetFullPath($configPath).ToUpperInvariant()
     $hash = [Convert]::ToHexString([Security.Cryptography.SHA256]::HashData([Text.Encoding]::UTF8.GetBytes($normalizedConfig)))
-    $resolutionStorePath = Join-Path $env:LOCALAPPDATA "AgentSandboxMcp\environment-resolutions\$hash.json"
-    Invoke-Step 'cli-executable-resolve-path' { & $agent executable resolve $pythonAlias --path $basePythonPath --config $configPath --lang ja }
-    Invoke-Step 'cli-executable-approve-runtime-root-yes' { & $agent executable approve $pythonAlias --path $basePythonPath --runtime-root $pythonRuntime --yes --config $configPath --lang ja }
-    Invoke-Step 'cli-shell-resolve-powershell' { & $agent executable resolve $powershellAlias --path $pwshPath --config $configPath --lang en }
-    Invoke-Step 'cli-shell-approve-runtime-root-yes' { & $agent executable approve $powershellAlias --path $pwshPath --runtime-root $pwshRuntime --yes --config $configPath --lang en }
-    Invoke-Step 'cli-shell-resolve-cmd' { & $agent executable resolve $cmdAlias --path $cmdPath --config $configPath --lang en }
-    Invoke-Step 'cli-shell-approve-cmd-no-runtime' { & $agent executable approve $cmdAlias --path $cmdPath --no-runtime --yes --config $configPath --lang en }
-    Invoke-Step 'cli-executable-list' { & $agent executable list --config $configPath --lang ja }
-    Invoke-Step 'cli-sandbox-show-text-default-format' { & $agent sandbox show --config $configPath --lang en }
-    Invoke-Step 'cli-sandbox-show-json' { & $agent sandbox show --format json --config $configPath --lang ja }
-    if ($CliOnly) {
-        Invoke-ExpectedFailure 'cli-check-detects-non-admin' @('check', '--config', $configPath, '--lang', 'ja')
-    }
-    else {
-        Invoke-Step 'cli-check' { & $agent check --config $configPath --lang ja }
-    }
+    $appliedStorePath = Join-Path $env:LOCALAPPDATA "AgentSandboxMcp\applied-configurations\$hash.json"
 
-    Invoke-ExpectedFailure 'cli-invalid-transport' @('serve', '--config', $configPath, '--transport', 'invalid')
-    Invoke-ExpectedFailure 'cli-invalid-format' @('sandbox', 'show', '--format', 'xml', '--config', $configPath)
-    Invoke-ExpectedFailure 'cli-management-missing-config' @('sandbox', 'resolve')
-    Invoke-ExpectedFailure 'cli-mutually-exclusive-runtime-options' @('executable', 'approve', $pythonAlias, '--path', $basePythonPath, '--runtime-root', $pythonRuntime, '--no-runtime', '--config', $configPath)
+    Invoke-Step 'cli-show-before-apply' { & $agent show $configPath }
+    Invoke-Step 'cli-apply-yes' { & $agent apply $configPath --yes }
+    Invoke-Step 'cli-show-applied' { & $agent show $configPath }
+    Invoke-ExpectedFailure 'removed-serve' @('serve')
+    Invoke-ExpectedFailure 'removed-check' @('check')
+    Invoke-ExpectedFailure 'removed-config-option' @('--config', $configPath)
+    Invoke-ExpectedFailure 'removed-language-option' @('--lang', 'ja')
+    Invoke-ExpectedFailure 'removed-transport-option' @('--transport', 'http')
+    Invoke-ExpectedFailure 'removed-executable-command' @('executable', 'list')
+    Invoke-ExpectedFailure 'removed-sandbox-command' @('sandbox', 'show')
 
     if (-not $CliOnly) {
-        Invoke-Step 'cli-serve-explicit-http' {
-            Start-And-ProbeServer $true
-            $script:server.Kill($true)
-            $script:server.WaitForExit()
-            $script:server = $null
-        }
-        Invoke-Step 'cli-serve-implicit-option-first' {
-            Start-And-ProbeServer $false
-            $script:server.Kill($true)
-            $script:server.WaitForExit()
-            $script:server = $null
+        Invoke-Step 'implicit-http-start' {
+            $script:server = Start-Process -FilePath $agent -ArgumentList @($configPath) -WorkingDirectory (Split-Path $agent) -WindowStyle Hidden -PassThru
+            $endpoint = "http://127.0.0.1:$httpPort/mcp"
+            for ($attempt=0; $attempt -lt 100; $attempt++) {
+                if ($script:server.HasExited) { throw "Server exited: $($script:server.ExitCode)" }
+                try { $response = Invoke-WebRequest -Uri $endpoint -Method Get -SkipHttpErrorCheck; if ($response.StatusCode -eq 405) { break } } catch { }
+                Start-Sleep -Milliseconds 100
+            }
+            if ($attempt -eq 100) { throw 'Server did not become ready.' }
+            $script:server.Kill($true); $script:server.WaitForExit(); $script:server = $null
         }
-
         $env:AGENT_MCP_MONKEY_ROOT = $testRootPath
         $env:AGENT_MCP_TEST_VENV_PYTHON = $venvPythonPath
         $env:AGENT_MCP_TEST_POWERSHELL = $pwshPath
-        $env:AGENT_MCP_TEST_POWERSHELL_RUNTIME = $pwshRuntime
+        $env:AGENT_MCP_TEST_POWERSHELL_RUNTIME = Split-Path $pwshPath
         $env:AGENT_MCP_TEST_CMD = $cmdPath
-        Invoke-Step 'readme-operational-windows-tests' {
-            & $windowsTests -class Agent.Windows.Tests.ReadmeOperationalTests -parallel none -failSkips
-        }
+        Invoke-Step 'readme-operational-windows-tests' { & $windowsTests -class Agent.Windows.Tests.ReadmeOperationalTests -parallel none -failSkips }
     }
-    Invoke-Step 'cli-executable-revoke-python' { & $agent executable revoke $pythonAlias --yes --config $configPath --lang ja }
-    Invoke-Step 'cli-executable-revoke-powershell' { & $agent executable revoke $powershellAlias --yes --config $configPath --lang en }
-    Invoke-Step 'cli-executable-revoke-cmd' { & $agent executable revoke $cmdAlias --yes --config $configPath --lang en }
-}
-finally {
+} finally {
     if ($server -and -not $server.HasExited) { $server.Kill($true); $server.WaitForExit() }
-    foreach ($alias in $aliases) {
-        & $agent executable revoke $alias --yes --config $configPath --lang en 2>$null | Out-Null
-    }
-    if ($resolutionStorePath -and (Test-Path -LiteralPath $resolutionStorePath)) { Remove-Item -LiteralPath $resolutionStorePath -Force }
+    if ($appliedStorePath -and (Test-Path -LiteralPath $appliedStorePath)) { Remove-Item -LiteralPath $appliedStorePath -Force }
     if (Test-Path -LiteralPath $runRoot) {
-        $resolvedRunRoot = (Resolve-Path -LiteralPath $runRoot).Path
-        if (-not $resolvedRunRoot.StartsWith($testRootPath.TrimEnd('\') + '\', [StringComparison]::OrdinalIgnoreCase)) {
-            throw 'Refusing to clean a test directory outside TestRoot.'
-        }
-        Remove-Item -LiteralPath $resolvedRunRoot -Recurse -Force
+        $resolved = (Resolve-Path -LiteralPath $runRoot).Path
+        if (-not $resolved.StartsWith($testRootPath.TrimEnd('\') + '\', [StringComparison]::OrdinalIgnoreCase)) { throw 'Refusing to clean outside TestRoot.' }
+        Remove-Item -LiteralPath $resolved -Recurse -Force
     }
     Remove-Item Env:AGENT_MCP_MONKEY_ROOT,Env:AGENT_MCP_TEST_VENV_PYTHON,Env:AGENT_MCP_TEST_POWERSHELL,Env:AGENT_MCP_TEST_POWERSHELL_RUNTIME,Env:AGENT_MCP_TEST_CMD -ErrorAction SilentlyContinue
 }