From 21e2e6346a2025a68529bb96c2bd5ffad9182861 Mon Sep 17 00:00:00 2001
From: Norin Lavaee <nlavaee@umich.edu>
Date: Thu, 2 Jul 2026 21:24:22 -0700
Subject: [PATCH 1/2] chore: add deepwiki MCP server config

Assistant-model: Claude Fable 5
---
 .mcp.json | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 .mcp.json

diff --git a/.mcp.json b/.mcp.json
new file mode 100644
index 000000000..214bd6808
--- /dev/null
+++ b/.mcp.json
@@ -0,0 +1,7 @@
+{
+    "mcpServers": {
+        "deepwiki": {
+            "url": "https://mcp.deepwiki.com/mcp"
+        }
+    }
+}

From 2083a530c50d3b13884f8d060a2d69ded207a642 Mon Sep 17 00:00:00 2001
From: Norin Lavaee <nlavaee@umich.edu>
Date: Thu, 2 Jul 2026 22:01:06 -0700
Subject: [PATCH 2/2] ci: run binary smoke tests from a clean temp cwd

The release-archive smoke steps invoked the built atomic binary with
--no-session from the repository checkout, so repo-local config (the
newly added root .mcp.json) was discovered at startup and the binary
hung connecting to the remote DeepWiki MCP server, stalling CI.

Run the --no-session smoke invocation from a clean RUNNER_TEMP working
directory in both test.yml and publish.yml (Linux and Windows) so
repo-local config can never leak into smoke runs.

Assistant-model: Claude Fable 5
---
 .github/workflows/publish.yml | 18 +++++++++++++++---
 .github/workflows/test.yml    | 14 +++++++++++++-
 2 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 90dd62dc1..e67e31802 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -85,9 +85,14 @@ jobs:
 
                   # --version exits before builtin extensions are loaded. Start the
                   # non-interactive runtime far enough to surface extension diagnostics,
-                  # but allow the expected no-models exit in CI.
+                  # but allow the expected no-models exit in CI. Run from a clean temp
+                  # cwd so repo-local config (e.g. .mcp.json) can't leak into the smoke
+                  # run and hang startup.
+                  work_dir="$RUNNER_TEMP/atomic-linux-binary-smoke-cwd"
+                  rm -rf "$work_dir"
+                  mkdir -p "$work_dir"
                   set +e
-                  output=$(printf '' | "$smoke_dir/atomic/atomic" --no-session 2>&1)
+                  output=$(cd "$work_dir" && printf '' | "$smoke_dir/atomic/atomic" --no-session 2>&1)
                   status=$?
                   set -e
                   echo "$output"
@@ -164,9 +169,16 @@ jobs:
 
                   # --version exits before builtin extensions are loaded. Start the
                   # non-interactive runtime far enough to surface extension diagnostics,
-                  # but allow the expected no-models exit in CI.
+                  # but allow the expected no-models exit in CI. Run from a clean temp
+                  # cwd so repo-local config (e.g. .mcp.json) can't leak into the smoke
+                  # run and hang startup.
+                  $workDir = Join-Path $env:RUNNER_TEMP "atomic-windows-binary-smoke-cwd"
+                  Remove-Item -Recurse -Force $workDir -ErrorAction SilentlyContinue
+                  New-Item -ItemType Directory -Path $workDir | Out-Null
+                  Push-Location $workDir
                   $output = "" | & $atomic --no-session 2>&1 | Out-String
                   $status = $LASTEXITCODE
+                  Pop-Location
                   Write-Host $output
                   if ($output -match "Failed to load extension") {
                     exit 1
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f33e14abf..ca372b3ec 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -95,8 +95,13 @@ jobs:
                       exit 1
                     }
                   done
+                  # Run from a clean temp cwd so repo-local config (e.g. .mcp.json)
+                  # can't leak into the smoke run and hang startup.
+                  work_dir="$RUNNER_TEMP/atomic-binary-smoke-cwd"
+                  rm -rf "$work_dir"
+                  mkdir -p "$work_dir"
                   set +e
-                  output=$(printf '' | "$smoke_dir/atomic/atomic" --no-session 2>&1)
+                  output=$(cd "$work_dir" && printf '' | "$smoke_dir/atomic/atomic" --no-session 2>&1)
                   status=$?
                   set -e
                   echo "$output"
@@ -145,8 +150,15 @@ jobs:
                       throw "Missing release archive path: $requiredPath"
                     }
                   }
+                  # Run from a clean temp cwd so repo-local config (e.g. .mcp.json)
+                  # can't leak into the smoke run and hang startup.
+                  $workDir = Join-Path $env:RUNNER_TEMP "atomic-binary-smoke-cwd"
+                  Remove-Item -Recurse -Force $workDir -ErrorAction SilentlyContinue
+                  New-Item -ItemType Directory -Path $workDir | Out-Null
+                  Push-Location $workDir
                   $output = "" | & $atomic --no-session 2>&1 | Out-String
                   $status = $LASTEXITCODE
+                  Pop-Location
                   Write-Host $output
                   if ($output -match "Failed to load extension") {
                     exit 1