Nucleic Control: spawn watchdog + reliable Stop + stdio diagnostics

Containerized control sessions could hang with no output ("Working…" forever): the agent's exec
stdio over the vminitd vsock channel intermittently failed to carry bytes, so claude ran and
reached the approval server but its stdin/stdout never connected — it idled in interactive
stream-json mode and never exited. Forensics (nucleic.sqlite + per-session claude-home MCP logs)
showed every stdio layer byte-identical to a working state, i.e. a flaky framework race, not a
regression in our code. Make the failure recoverable and visible instead of an eternal spinner:

- ClaudeCodeBackend: a 60s spawn watchdog on containerized runs — no first stdout → emit a
  recoverable error (with guest stderr + container probe), SIGKILL the wedged process, and finish
  the run errored, instead of awaiting stdoutLines forever.
- Stop reliability: ProcessHandle.forceCloseStreams() (ContainerizedProcessHandle finishes its
  line streams host-side; default no-op for the host pipe handle), wired into every kill
  escalation (terminate/interruptThenKill/killGroupAfter) so a force-killed run always settles
  even when the guest wait/stdio RPC wedges — the real cause of "Stop is inconsistent".
- Cap MCP_TIMEOUT (connection) to 60s so an unreachable approval server can't wedge startup for
  ~24.8 days; MCP_TOOL_TIMEOUT stays unbounded for human-answered approvals.
- LinuxProcess.setupIO logs which stdio stream fails to connect (os.Logger, com.nucleic /
  container-io) so a stall pinpoints the failing stream. Vendored patch #3.
- Tests: stop-escalation force-close, responsive-process no-op, MCP timeout asymmetry.

Co-Authored-By: Claude Opus 4.8 <[email protected]>

PATCHES.md

@@ -29,7 +29,15 @@ in-tree means the patch can't be lost to a dependency re-resolve.
    which let a forked child survive a Stop in a long-lived shared container. Marked with
    `[Nucleic vendored patch]`; used by `ContainerizedProcessHandle.sendSignal` in NucleicCore.
 
-3. **Trimmed for footprint (no behavior change).** `Tests/`, `docs/`, `examples/`, and `images/`
+3. **`Sources/Containerization/LinuxProcess.swift` — stdio-connection diagnostics (log-only).**
+   `setupIO` logs (`os.Logger`, subsystem `com.nucleic`, category `container-io`) when a *configured*
+   stdio stream's guest side never connects — which leaves its host `FileHandle` nil, so the relay /
+   readability handler is never wired and the agent's stdin is never delivered (it hangs) or its
+   stdout is never read (the "no output, just a spinner" symptom in Nucleic Control containers).
+   Behavior is unchanged; it only surfaces the failing stream. Marked `[Nucleic vendored patch]`
+   (the `import os`, the `nucleicIOLog` static, and the per-stream check in `setupIO`).
+
+4. **Trimmed for footprint (no behavior change).** `Tests/`, `docs/`, `examples/`, and `images/`
    were dropped, and the corresponding `.testTarget(...)` entries removed from `Package.swift`. The
    library/executable targets we build are untouched.
 
@@ -38,9 +46,10 @@ in-tree means the patch can't be lost to a dependency re-resolve.
 1. `git clone` upstream (or copy `.build/checkouts/containerization` after bumping the URL pin
    temporarily), check out the desired commit.
 2. `rsync -a --exclude=.git --exclude=.build --exclude=.swiftpm --exclude=Tests/ --exclude=docs/ \
-   --exclude=examples/ --exclude=images/ <upstream>/ third_party/containerization/`
+   --exclude=images/ <upstream>/ third_party/containerization/`
 3. Remove the `.testTarget(...)` blocks from `third_party/containerization/Package.swift`.
-4. Re-apply patch #1 (the `vmExtensions` field + the `vmConfig.extensions = …` forward) and patch
-   #2 (`LinuxProcess.killProcessGroup(_:)`). Grep for `[Nucleic vendored patch]` to find every site.
+4. Re-apply patch #1 (the `vmExtensions` field + the `vmConfig.extensions = …` forward), patch #2
+   (`LinuxProcess.killProcessGroup(_:)`), and patch #3 (the `setupIO` stdio-connection log + its
+   `import os` / `nucleicIOLog`). Grep for `[Nucleic vendored patch]` to find every site.
 5. Update the commit hash above and in the root `Package.swift` comment.
 6. `swift build` and run the balloon tests.

Sources/Containerization/LinuxProcess.swift

@@ -21,10 +21,14 @@ import ContainerizationOS
 import Foundation
 import Logging
 import Synchronization
+import os  // [Nucleic vendored patch] stdio-connection diagnostics
 
 /// `LinuxProcess` represents a Linux process and is used to
 /// setup and control the full lifecycle for the process.
 public final class LinuxProcess: Sendable {
+    /// [Nucleic vendored patch] Diagnostic log for stdio stream-connection failures (see `setupIO`).
+    static let nucleicIOLog = os.Logger(subsystem: "com.nucleic", category: "container-io")
+
     /// The ID of the process. This is purely metadata for the caller.
     public let id: String
 
@@ -97,7 +101,7 @@ public final class LinuxProcess: Sendable {
     private let agent: any VirtualMachineAgent
     private let vm: any VirtualMachineInstance
     private let ociRuntimePath: String?
-    private let logger: Logger?
+    private let logger: Logging.Logger?  // [Nucleic vendored patch] disambiguated from os.Logger
     private let onDelete: (@Sendable () async -> Void)?
 
     init(
@@ -108,7 +112,7 @@ public final class LinuxProcess: Sendable {
         ociRuntimePath: String?,
         agent: any VirtualMachineAgent,
         vm: any VirtualMachineInstance,
-        logger: Logger?,
+        logger: Logging.Logger?,  // [Nucleic vendored patch] disambiguated from os.Logger
         onDelete: (@Sendable () async -> Void)? = nil
     ) {
         self.id = id
@@ -146,6 +150,18 @@ extension LinuxProcess {
             }
         }
 
+        // [Nucleic vendored patch] Diagnostics: a configured stdio stream whose guest side never
+        // connected leaves its host FileHandle `nil`, so the relay / readability handler below is
+        // never wired — the agent's stdin is then never delivered (it hangs waiting for input) or
+        // its stdout is never read ("no output, just a spinner"). Log that specific failure (Console
+        // / `log show`, subsystem com.nucleic, category container-io) so a stall pinpoints the stream
+        // instead of proceeding silently. Log-only; behavior is unchanged.
+        let configured = [self.ioSetup.stdin != nil, self.ioSetup.stdout != nil, self.ioSetup.stderr != nil]
+        for (index, label) in [(0, "stdin"), (1, "stdout"), (2, "stderr")] where configured[index] && handles[index] == nil {
+            Self.nucleicIOLog.error(
+                "setupIO[\(self.id, privacy: .public)]: \(label, privacy: .public) stream never connected from the guest — agent stdio will stall")
+        }
+
         // Note: stdin relay is started separately via startStdinRelay() after
         // the process has started, to avoid a deadlock where closeStdin is
         // called before the process is consuming from the pipe.