Enhance service lifecycle management, cohort handling, and status synchronization:

- Add `registerCohortUpdates` for tracking geometry changes in cohorts.
- Refactor `ServiceMonitor` with improved client status handling and local service shutdown coordination.
- Introduce `stopRequested` flag for process stop management in `LocalInstanceImpl`.
- Add methods for geometry retrieval and validation across services.
- Improve `refreshStatus` and `refreshClientStatus` synchronization logic.

Author: fvilla

klab.core.api/src/main/java/org/integratedmodelling/klab/api/configuration/Setting.java

@@ -298,6 +298,11 @@ public enum Setting {
       "Launch a DevToolsFX debugging tool for the GUI when in graphical mode",
       Map.class,
       Map.of()),
+  LIST_LOCAL_COMMIT_OPERATIONS(
+      Page.DEBUGGING,
+      "List local commit/push operations in project team actions",
+      Boolean.class,
+      Boolean.FALSE),
   CLEAR_WORKSPACE(
       Page.RESOURCES,
       "Execute to remove all workspaces from the service. This is a destructive operation.",

klab.core.api/src/main/java/org/integratedmodelling/klab/api/services/KlabService.java

@@ -231,6 +231,7 @@ default boolean hasChangedComparedTo(ServiceStatus statusBeforeChecking) {
           || this.isBusy() != statusBeforeChecking.isBusy()
           || this.isConnected() != statusBeforeChecking.isConnected()
           || this.isOperational() != statusBeforeChecking.isOperational()
+          || this.isShutdown() != statusBeforeChecking.isShutdown()
           || !this.getAdvisories().equals(statusBeforeChecking.getAdvisories());
     }
 

klab.core.common/src/main/java/org/integratedmodelling/common/distribution/LocalInstanceImpl.java

@@ -5,6 +5,7 @@
 import java.nio.file.Files;
 import java.util.EnumSet;
 import java.util.Map;
+import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.atomic.AtomicReference;
 import org.apache.commons.exec.CommandLine;
 import org.apache.commons.exec.DefaultExecuteResultHandler;
@@ -31,6 +32,7 @@ public abstract class LocalInstanceImpl implements LocalInstance {
   protected final Stack.Tag tag;
 
   protected AtomicReference<Status> status = new AtomicReference<>(Status.UNKNOWN);
+  protected AtomicBoolean stopRequested = new AtomicBoolean(false);
   protected DefaultExecutor executor;
   protected ExecuteWatchdog watchdog;
   protected ExecuteStreamHandler streamHandler;
@@ -126,8 +128,7 @@ private void monitorAlreadyRunningProcess(long pid) {
                   .thenAccept(
                       p -> {
                         if (this.pid != null && this.pid.equals(p.pid())) {
-                          this.status.set(Status.STOPPED);
-                          cleanupState();
+                          markStopped();
                         }
                       });
             });
@@ -161,6 +162,7 @@ public void setStreamHandler(ExecuteStreamHandler streamHandler) {
   @Override
   public boolean forceRestart(Option... options) {
     stop();
+    waitForStop();
     return start(options);
   }
 
@@ -170,11 +172,15 @@ public synchronized boolean start(Option... options) {
     if (status.get() == Status.RUNNING) {
       return true;
     }
+    if (status.get() == Status.WAITING) {
+      return false;
+    }
 
     CommandLine commandLine = getCommandLine(product, settings);
     if (commandLine == null) {
       return false;
     }
+    stopRequested.set(false);
 
     EnumSet<Option> startOptions = EnumSet.noneOf(Option.class);
     if (options != null) {
@@ -220,15 +226,17 @@ protected Process launch(
           @Override
           public void onProcessComplete(int exitValue) {
             super.onProcessComplete(exitValue);
-            status.set(Status.STOPPED);
-            cleanupState();
+            markStopped();
           }
 
           @Override
           public void onProcessFailed(ExecuteException e) {
             super.onProcessFailed(e);
-            status.set(Status.ERROR);
-            cleanupState();
+            if (stopRequested.get()) {
+              markStopped();
+            } else {
+              markError();
+            }
           }
         };
 
@@ -267,6 +275,11 @@ private void cleanupState() {
   @Override
   public synchronized boolean stop() {
     if (watchdog != null) {
+      stopRequested.set(true);
+      status.set(Status.WAITING);
+      if (pid != null) {
+        monitorAlreadyRunningProcess(pid);
+      }
       watchdog.destroyProcess();
       watchdog = null;
       executor = null;
@@ -276,9 +289,18 @@ public synchronized boolean stop() {
       return true;
     }
     if (pid != null) {
-      ProcessHandle.of(pid).ifPresent(ProcessHandle::destroy);
-      cleanupState();
-      status.set(Status.STOPPED);
+      var stoppedPid = pid;
+      var processHandle = ProcessHandle.of(stoppedPid);
+      if (processHandle.isPresent() && processHandle.get().isAlive()) {
+        stopRequested.set(true);
+        status.set(Status.WAITING);
+        monitorAlreadyRunningProcess(stoppedPid);
+        if (!processHandle.get().destroy()) {
+          processHandle.get().destroyForcibly();
+        }
+      } else {
+        markStopped();
+      }
       process = null;
       inputStream = null;
       outputStream = null;
@@ -287,6 +309,36 @@ public synchronized boolean stop() {
     return false;
   }
 
+  private void waitForStop() {
+    long deadline = System.currentTimeMillis() + 10000;
+    while (status.get() == Status.WAITING && System.currentTimeMillis() < deadline) {
+      try {
+        Thread.sleep(100);
+      } catch (InterruptedException e) {
+        Thread.currentThread().interrupt();
+        return;
+      }
+    }
+  }
+
+  private synchronized void markStopped() {
+    stopRequested.set(false);
+    status.set(Status.STOPPED);
+    cleanupState();
+    watchdog = null;
+    executor = null;
+    process = null;
+  }
+
+  private synchronized void markError() {
+    stopRequested.set(false);
+    status.set(Status.ERROR);
+    cleanupState();
+    watchdog = null;
+    executor = null;
+    process = null;
+  }
+
   @Override
   public OutputStream getOutputStream() {
     return process != null ? outputStream : null;

klab.core.common/src/main/java/org/integratedmodelling/common/services/client/BaseServiceClient.java

@@ -139,12 +139,28 @@ public boolean isLocal() {
   public boolean shutdown() {
     int refCount = monitor.release(this);
     if (refCount == 0 && monitor.isLocal()) {
+      // FIXME needs the admin user scope
+      return requestShutdown();
+    }
+    return false;
+  }
+
+  /**
+   * Ask the service process to shut down without unregistering this client from status monitoring.
+   */
+  public boolean requestShutdown() {
+    if (monitor.isLocal()) {
       // FIXME needs the admin user scope
       return client.withScope(serviceScope).put(ServicesAPI.ADMIN.SHUTDOWN, null, Boolean.class);
     }
     return false;
   }
 
+  /** Poll status immediately and return the monitor's current status without unregistering. */
+  public ServiceStatus refreshStatus() {
+    return monitor.refreshStatus();
+  }
+
   @Override
   public String declareSessionScope(
       SessionScope sessionScope, UserScope userScope, KActorsBehavior behavior) {

klab.core.common/src/main/java/org/integratedmodelling/common/services/client/ServiceClientCatalog.java

@@ -47,7 +47,7 @@ public class ClientMonitor {
     private final boolean local;
     private ScheduledFuture<?> schedule;
 
-    private Set<BaseServiceClient> registeredClients = new HashSet<>();
+    private Set<BaseServiceClient> registeredClients = ConcurrentHashMap.newKeySet();
 
     public Utils.Http.Client getClient() {
       return client;
@@ -112,19 +112,26 @@ void connect() {
     }
 
     void timedTasks() {
+      refreshStatus(true);
+    }
+
+    public KlabService.ServiceStatus refreshStatus() {
+      return refreshStatus(false);
+    }
+
+    synchronized KlabService.ServiceStatus refreshStatus(boolean notifyListeners) {
 
       //        if (settings != null && "off".equals(settings.get(Setting.POLLING, String.class))) {
       //            return;
       //        }
 
-      if (!client.isAlive()) {
-        this.status.set(KlabService.ServiceStatus.offline(type, serverId));
-        return;
-      }
-
       var statusBeforeChecking = status.get();
       try {
-        readStatus();
+        if (!client.isAlive()) {
+          this.status.set(KlabService.ServiceStatus.offline(type, serverId));
+        } else {
+          readStatus();
+        }
       } finally {
 
         boolean statusHasChanged =
@@ -140,13 +147,17 @@ void timedTasks() {
             serviceClients.put(serverId, this);
           }
 
-          for (var client : registeredClients) {
-            for (var listener : client.statusListeners) {
-              listener.accept(status.get(), statusHasChanged);
+          if (notifyListeners) {
+            for (var client : registeredClients) {
+              for (var listener : client.statusListeners) {
+                listener.accept(status.get(), statusHasChanged);
+              }
             }
           }
         }
       }
+
+      return status.get();
     }
 
     void readStatus() {
@@ -160,7 +171,9 @@ void readStatus() {
     }
 
     private void close() {
-      this.schedule.cancel(true);
+      if (this.schedule != null) {
+        this.schedule.cancel(true);
+      }
       serviceClients.remove(serverId);
     }