Add geometry handling for cohorts and fix spatial layer removal logic. Update domain color scheme.

Author: Ferdinando Villa

klab.core.api/src/main/java/org/integratedmodelling/klab/api/data/RepositoryState.java

@@ -67,31 +67,27 @@ public enum Operation {
      * Fetch any remote changes, if no conflicts merge them, then commit the current changes and
      * pull
      */
-    FETCH_COMMIT_AND_PUSH,
+    SYNC_AND_PUBLISH,
     /** Fetch remote changes and merge them if no conflicts arise */
-    FETCH_AND_MERGE,
+    GET_LATEST,
     /** Commit current local changes without contacting the remote repository */
     SAVE_CHANGES,
     /** Push committed local changes to the remote repository */
     PUBLISH_CHANGES,
     /** Switch to another branch (possibly new) after locally committing any pending changes */
     COMMIT_AND_SWITCH,
     /** Hard reset head deleting all uncommitted changes */
-    HARD_RESET,
-    /** Friendlier alias for HARD_RESET */
     DISCARD_LOCAL_CHANGES,
 
     MERGE_CHANGES_FROM;
 
     public String description() {
       return switch (this) {
-        case FETCH_COMMIT_AND_PUSH ->
-            "Fetch remote changes, merge if no conflicts, commit and push";
-        case FETCH_AND_MERGE -> "Fetch remote changes, merge if no conflicts";
-        case SAVE_CHANGES -> "Save current local changes";
-        case PUBLISH_CHANGES -> "Publish committed changes";
+        case SYNC_AND_PUBLISH -> "Fetch remote changes, merge if no conflicts, commit and push";
+        case GET_LATEST -> "Fetch remote changes, merge if no conflicts";
+        case SAVE_CHANGES -> "Accept all changes to local repository without publishing";
+        case PUBLISH_CHANGES -> "Publish locally committed changes";
         case COMMIT_AND_SWITCH -> "Commit changes and switch to another branch";
-        case HARD_RESET -> "Hard reset, deleting all uncommitted changes";
         case DISCARD_LOCAL_CHANGES -> "Discard local uncommitted changes";
         case MERGE_CHANGES_FROM -> "Merge changes from another branch";
       };

klab.services.resources/src/main/java/org/integratedmodelling/klab/services/resources/storage/WorkspaceManager.java

@@ -309,14 +309,14 @@ public List<ResourceSet> manageRepository(
 
       var mods =
           switch (operation) {
-            case FETCH_COMMIT_AND_PUSH ->
+            case SYNC_AND_PUBLISH ->
                 Utils.Git.fetchCommitAndPush(
                     fileProjectStorage.getRootFolder(),
                     arguments == null || arguments.length == 0
                         ? "Committed by k.LAB resources " + "service"
                         : arguments[0],
                     scope);
-            case FETCH_AND_MERGE ->
+            case GET_LATEST ->
                 Utils.Git.fetchAndMerge(fileProjectStorage.getRootFolder(), scope);
             case SAVE_CHANGES ->
                 Utils.Git.commitChanges(
@@ -328,7 +328,6 @@ public List<ResourceSet> manageRepository(
             case PUBLISH_CHANGES -> Utils.Git.pushChanges(fileProjectStorage.getRootFolder(), scope);
             case COMMIT_AND_SWITCH ->
                 Utils.Git.commitAndSwitch(fileProjectStorage.getRootFolder(), arguments[0], scope);
-            case HARD_RESET -> Utils.Git.hardReset(fileProjectStorage.getRootFolder());
             case DISCARD_LOCAL_CHANGES -> Utils.Git.hardReset(fileProjectStorage.getRootFolder());
             case MERGE_CHANGES_FROM ->
                 Utils.Git.mergeChangesFrom(fileProjectStorage.getRootFolder(), arguments[0]);