diff --git a/scripts/tier2/setup_tier2_clone.ps1 b/scripts/tier2/setup_tier2_clone.ps1
index 7b0c38b9..16cb4ffd 100644
--- a/scripts/tier2/setup_tier2_clone.ps1
+++ b/scripts/tier2/setup_tier2_clone.ps1
@@ -83,8 +83,36 @@ if ($PSCmdlet.ShouldProcess("Bootstrap Tier 2 clone at $Tier2ClonePath")) {
             $existing | ConvertTo-Json -Depth 10 | Set-Content $cloneConfig
         } else {
             Copy-Item -Force "$MainRepoPath\conductor\tier2\opencode.json.fragment" $cloneConfig
+            $existing = $fragment
         }
 
+        # Override the MCP server's command + PYTHONPATH to point at the
+        # Tier 2 clone's files. The inherited config points to the main
+        # repo's scripts/mcp_server.py, which loads the main repo's
+        # project_root (C:\projects\manual_slop) and reads the main repo's
+        # mcp_paths.toml (which allowlists C:\projects\gencpp). When Tier 2
+        # calls manual-slop_read_file on a clone path, the MCP server
+        # rejects it with "Allowed base directories are: manual_slop, gencpp".
+        # The fix: launch the MCP server from the clone's path with the
+        # clone's PYTHONPATH, and replace the clone's mcp_paths.toml with
+        # an empty one so the clone's MCP server has no extra_dirs.
+        if ($existing.mcp -and $existing.mcp.'manual-slop') {
+            $existing.mcp.'manual-slop'.command = @(
+                "$env:USERPROFILE\scoop\apps\uv\current\uv.exe",
+                "run",
+                "python",
+                "$Tier2ClonePath\scripts\mcp_server.py"
+            )
+            $existing.mcp.'manual-slop'.environment.PYTHONPATH = "$Tier2ClonePath\src"
+            $existing | ConvertTo-Json -Depth 10 | Set-Content $cloneConfig
+        }
+        $cloneMcpPaths = "$Tier2ClonePath\mcp_paths.toml"
+        @"
+[allowed_paths]
+extra_dirs = []
+"@ | Set-Content -Path $cloneMcpPaths -NoNewline
+        Write-Host "[tier2-bootstrap] MCP server pointed at clone; mcp_paths.toml reset to empty extra_dirs"
+
         # 4. Install git hooks
         Write-Host "[tier2-bootstrap] installing git hooks"
         Copy-Item -Force "$MainRepoPath\conductor\tier2\githooks\pre-push" "$Tier2ClonePath\.git\hooks\pre-push"
diff --git a/tests/test_tier2_setup_bootstrap.py b/tests/test_tier2_setup_bootstrap.py
index e30b78dc..33ac1c14 100644
--- a/tests/test_tier2_setup_bootstrap.py
+++ b/tests/test_tier2_setup_bootstrap.py
@@ -37,3 +37,18 @@ def test_bootstrap_whatif_does_not_create_clone(tmp_path: Path) -> None:
  assert result.returncode == 0, f"pwsh exit {result.returncode}\nstdout={result.stdout}\nstderr={result.stderr}"
  assert "What if" in result.stdout or "starting bootstrap" in result.stdout or "Bootstrap Tier 2 clone" in result.stdout
  assert not fake_clone.exists(), "-WhatIf should not have created the clone"
+
+
+def test_setup_script_overrides_mcp_server() -> None:
+ """Regression test: setup_tier2_clone.ps1 MUST override the MCP server's
+ command and PYTHONPATH to point at the Tier 2 clone, AND reset the
+ clone's mcp_paths.toml to empty extra_dirs. Otherwise the clone inherits
+ the main repo's MCP config (which has manual_slop's path and an
+ mcp_paths.toml allowlisting gencpp), leading to 'ACCESS DENIED' on clone
+ paths (2026-06-17 bug)."""
+ script = Path("scripts/tier2/setup_tier2_clone.ps1").resolve()
+ content = script.read_text(encoding="utf-8")
+ assert "mcp.'manual-slop'.command" in content, "script must override MCP server command"
+ assert "mcp.'manual-slop'.environment.PYTHONPATH" in content, "script must override MCP server PYTHONPATH"
+ assert "mcp_paths.toml" in content, "script must reset mcp_paths.toml"
+ assert "extra_dirs = []" in content, "script must set extra_dirs to empty"