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.

1 files changed, 15 insertions, 19 deletions

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 }
 }